Use of mTOR Inhibitors to Enhance T Cell Immune Responses

ABSTRACT

It is disclosed herein that treatment of a subject with an mTOR inhibitor enhances antigen-specific T cell immune responses. Thus, provided herein is a method of enhancing an antigen-specific T cell response in a subject by administering to the subject a therapeutically effective amount of an mTOR inhibitor. The antigen can be any antigen, such as an antigen from a pathogen or a vaccine, or a tumor antigen. In some embodiments, the method further comprises administering to the subject a vaccine, such as a virus vaccine or a cancer vaccine. The mTOR inhibitor can be administered either before or after vaccination to enhance the quantity and quality of the T cell immune response and immunological memory. In some examples, the mTOR inhibitor is rapamycin or a rapamycin analog.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a division of U.S. application Ser. No. 14/468,087 filed Aug. 25, 2014, which is a division of U.S. application Ser. No. 13/057,057 filed Feb. 1, 2011 that granted as U.S. Pat. No. 8,840,899 on Sep. 23, 2014, which is the National Stage of International Application No. PCT/US2009/052886 filed Aug. 5, 2009, which claims the benefit of priority to U.S. Provisional Application No. 61/086,350 filed Aug. 5, 2008. The entirety of each of these applications is hereby incorporated by reference for all purposes.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under grant numbers 5R37AI030048 and 5P01AI044644 awarded by the National Institutes of Health. The government has certain rights in the invention.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED AS A TEXT FILE VIA THE OFFICE ELECTRONIC FILING SYSTEM (EFS-WEB)

The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 08100USDIV2_ST25.txt. The text file is 78 KB, was created on May 16, 2016, and is being submitted electronically via EFS-Web.

FIELD

This disclosure concerns the use of mammalian target of rapamycin (mTOR) inhibitors, such as rapamycin or analogs thereof, to enhance T cell immune responses.

BACKGROUND

Mammalian target of rapamycin (mTOR) is a serine/threonine protein kinase known to play a role in regulating cell growth, cell proliferation, cell motility, cell survival, protein synthesis and transcription. Dysregulation of the mTOR pathway is implicated as a contributing factor to various human diseases, particularly various types of cancer. Rapamycin is a natural product produced by the bacterium Streptomyces hygroscopicus that can inhibit mTOR through association with its intracellular receptor FK-506 binding protein 12 (FKBP12). The FKBP12-rapamycin complex binds directly to the FKBP12-rapamycin binding domain of mTOR.

It has been demonstrated that mTOR functions as a catalytic subunit for two distinct molecular complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2). In addition to mTOR, mTORC1 is composed of regulatory associated protein of mTOR (Raptor) and mammalian LST8/G-protein β-subunit like protein (mLST8/GβL). This complex functions as a nutrient/energy/redox sensor and plays a role in regulating protein synthesis. The activity of mTORC1 is stimulated by insulin, growth factors, serum, phosphatidic acid, amino acids (particularly leucine) and oxidative stress (Hay and Sonenberg, Genes Dev. 18(16):1926-1945, 2004; Wullschleger et al., Cell 124(3):471-484). In contrast, mTORC1 is known to be inhibited by low nutrient levels, growth factor deprivation, reductive stress, caffeine, rapamycin, farnesylthiosalicylic acid and curcumin (Beevers et al., Int. J. Cancer 119(4):757-764, 2006; McMahon et al., Mol. Endocrinol. 19(1):175-183). The components of mTORC2 are rapamycin-insensitive companion of mTOR (Rictor), GβL, mammalian stress-activated protein kinase interacting protein 1 and mTOR. mTORC2 has been shown to function as an important regulator of the cytoskeleton through its stimulation of F-actin stress fibers, paxillin, RhoA, Rac1, Cdc42 and protein kinase C alpha (Sarbassov et al., Curr. Biol. 14(14): 1296-302, 2004; Sarbassov et al., Science 307(5712): 1098-101, 2005). Unlike mTORC1, mTORC2 is not sensitive to rapamycin.

A number of mTOR inhibitors are currently being used, or are currently being investigated in clinical trials, to treat a variety of conditions. Inhibitors of mTOR, such as rapamycin, are known to exhibit immunosuppressive and anti-proliferative properties. Accordingly, mTOR inhibitors are routinely administered to transplant recipients to prevent organ or bone marrow rejection.

Vaccines are widely used to treat or prevent disease, including infectious disease and cancer. In order for a vaccine to be effective, sufficient immunological memory against the target pathogen or cancer must be elicited, which often requires more than one dose of vaccine. The ability to induce adequate immunological memory in a subject by administration of a single vaccine dose is desirable to achieve rapid vaccination, as well as to reduce cost and improve compliance. Thus, a need remains for methods of enhancing immune responses against candidate vaccines.

SUMMARY

As disclosed herein, mTOR inhibitors have surprisingly been demonstrated to enhance antigen-specific T cell immune responses, which are critical for establishing immunity. To enhance antigen-specific T cell immune responses in a subject exposed to an antigen, an mTOR inhibitor is administered during the contraction phase of a T cell response, or the inhibitor is administered at any time prior to or subsequent to antigen challenge when administered at a low dose.

Provided herein is a method of enhancing an antigen-specific T cell response in a subject by administering to the subject a therapeutically effective amount of an antigen and a therapeutically effective amount of an mTOR inhibitor, thereby enhancing an antigen-specific T cell immune response in the subject. In some embodiments, enhancing an antigen-specific T cell response in a subject includes increasing the number or quality of antigen-specific T cells in the subject. In some embodiments, the antigen is part of a vaccine. The antigen can be any antigen, including, but not limited to, an antigen from a pathogen, such as a virus, bacteria, fungus or parasite, or a tumor antigen.

Also provided is a method of increasing the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells in a subject by administering to the subject a therapeutically effective amount of an antigen and an mTOR inhibitor. Further provided is a method of increasing expression of CD127, CD62L, Bcl-2 and CD27, and decreasing expression of KLRG-1, in CD8+ T cells of a subject by administering to the subject an antigen and an mTOR inhibitor.

The foregoing and other features and advantages will become more apparent from the following detailed description of several embodiments, which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a schematic model of virus-specific CD8⁺ T cell responses during an acute viral infection. Virus-specific CD8⁺ T cells expand upon viral infection and become effector T cells. The expansion phase is followed by a contraction phase in which 90-95% of the effector cells die. The remaining effector cells differentiate into memory T cells during the contraction phase, and these memory cells further differentiate into high quality memory T cells during the maintenance phase.

FIG. 2A is a schematic of the experimental design for testing the effect of rapamycin treatment on virus-specific CD8⁺ T cells during the expansion phase. Mice were infected with lymphocytic choriomeningitis virus (LCMV) on Day 0 and treated with rapamycin every day starting one day prior to infection (Day −1). Peripheral blood mononuclear cells (PBMCs) from untreated (No Rapa) and rapamycin-treated (Rapa Tx) mice were analyzed on Day 8. FIG. 2B shows fluorescence activated cell sorting (FACS) plots of PBMCs obtained from untreated and rapamycin-treated mice. PBMCs were stained with LCMV GP33 epitope-specific tetramer DbGP33, anti-CD8 and anti-CD44. The percentage of virus-specific CD8⁺ T cells is indicated. FIG. 2C is a graph showing LCMV titers in rapamycin-treated and untreated mice.

FIG. 3A is a schematic of the experimental design for testing the effect of rapamycin treatment on virus-specific CD8⁺ T cells during the maintenance phase. Carboxyfluorescein succinimidyl ester (CFSE)-labeled GP33-epitope specific memory CD8⁺ T cells were adoptively transferred into mice on Day 0. Mice were treated with rapamycin every day starting one day prior to adoptive transfer (Day −1). Splenocytes from untreated and rapamycin-treated mice were analyzed on Day 42. FIG. 3B is a graph showing the number of virus-specific CD8⁺ T cells in the spleen of untreated and rapamycin-treated mice on Day 42. FIG. 3C shows FACS plots of CFSE-labeled virus-specific CD8⁺ T cells obtained from untreated and rapamycin-treated mice on Day 42 post-transfer. The percentage of adoptively transferred cells that divided more than twice is indicated.

FIG. 4A is a schematic of the experimental design for testing the effect of rapamycin treatment on virus-specific CD8⁺ T cells during the contraction phase. Mice were infected with LCMV on Day 0 and treated with rapamycin starting on Day 8 after infection. Splenocytes from untreated and rapamycin-treated mice were analyzed on Day 35. FIG. 4B is a graph showing the number of virus-specific CD8⁺ T cells obtained from the spleen of untreated and rapamycin-treated mice. Tetramer staining was used to detect GP33, GP276 and NP396 epitope-specific CD8⁺ T cells, while CD8⁺ T cells specific for epitopes NP205 and GP118 were detected by IFN-γ staining following peptide stimulation.

FIG. 5A shows a series of FACS plots evaluating expression of T cell markers (CD127, CD62L, KLRG-1, CD27 and Bcl-2) on splenocytes obtained from untreated and rapamycin-treated mice according to the procedure shown in FIG. 4A. FIG. 5B is a series of graphs that summarizes the phenotype of DbGP33, DbGP276 and DbNP396 tetramer-positive CD8⁺ T cells.

FIG. 6 is a series of graphs showing that rapamycin treatment induces high quality memory T cells during the contraction phase in PBMCs, liver and lymph nodes (LN).

FIG. 7A is a schematic of the experimental design for demonstrating that rapamycin treatment enhances CD62L re-expression during the T cell contraction phase. LCMV-specific transgenic (P14) effector CD8⁺ T cells (Thy-1.1⁺) were isolated on Day 8 post-infection. CD62L^(high) cells were depleted from the isolated effector P14 cells and the remaining CD62L^(low) effector CD8⁺ T cells were transferred into Thy-1.2⁺ naïve mice. Mice were then treated with rapamycin daily. FIG. 7B is a graph showing conversion of CD62L expression from low to high in PBMC from Day 0 to Day 26 post-transfer. FIG. 7C is a graph showing the number of CD62L^(high) P14 cells in the spleen of untreated and rapamycin-treated mice on Day 26 post-transfer. FIG. 7D shows FACS plots of CD62L expression of Thy-1.1⁺ P14 cells on Day 26 post-transfer. The percentage of cells that are CFSE^(high) (cells that have not divided) and CD62L^(high) is indicated.

FIG. 8A is a schematic of the experimental design for evaluating protective immunity by rapamycin-induced memory CD8⁺ T cells. CD62L^(Low) LCMV-specific Day 8 effector P14 cells were transferred into naïve mice on Day 0 and mice were treated with rapamycin for 25 days. Mice were challenged with vaccinia virus (VV) GP33 on Day 28. FIG. 8B shows FACS plots of splenocytes obtained from untreated and rapamycin-treated mice on Day 5 post-challenge. The percentage of DbGP33 tetramer-positive P14 cells is indicated. FIG. 8C is a graph showing the number of DbGP33 tetramer-positive P14 cells in the spleen of untreated and rapamycin-treated mice on Day 5 post-challenge. FIG. 8D is a graph showing viral titer in the ovaries (PFU/gram) of naïve, untreated and rapamycin-treated mice on Day 5 post-challenge.

FIG. 9A is a schematic of the experimental design for evaluating homeostatic proliferation of rapamycin-induced memory CD8⁺ T cells. CFSE-labeled P14 memory cells derived from rapamycin-treated or untreated mice were adoptively transferred into naïve mice and analyzed up to 30 days post-transfer. FIG. 9B is a graph showing the percentage of divided P14 memory cells in PBMC over time. FIG. 9C shows FACS plots of CFSE-labeled CD8⁺ T cells obtained from the spleen of untreated and rapamycin-treated mice on Day 30 post-transfer. The percentage of P14 cells that divided more than twice is indicated.

FIG. 10A is a schematic of the experimental design to demonstrate that rapamycin treatment enhances high quality memory T cells during the contraction phase of recall responses. LCMV-specific memory P14 cells were transferred into naïve mice on Day −1. The next day, mice were infected with VVgp33 and either untreated or treated with rapamycin daily from Day 8 post-infection. FIG. 10B is a graph showing the number of P14 cells in the spleen of untreated and rapamycin-treated mice on Day 31. FIG. 10C is a series of FACS plots showing the phenotypic differences of P14 cells on Day 31 post-infection in the spleen, as measured by expression of high quality T cell markers CD127, CD62L, KLRG-1, CD27 and Bcl-2.

FIG. 11A is a schematic of the experimental design to demonstrate that low dose rapamycin treatment enhances the number of virus-specific CD8⁺ T cells. Rapamycin treatment was initiated one day prior to infection with LCMV. FIG. 11B is a graph showing the number of DbGP33 tetramer-positive LCMV-specific CD8⁺ T responses in PBMC obtained from untreated and rapamycin-treated mice up to 30 days post-infection. FIG. 11C is a graph showing the number of virus-specific CD8⁺ T cells in the spleen of untreated and rapamycin-treated mice at Day 35. Tetramer staining was used to detect GP33, GP276 and NP396 epitope-specific CD8⁺ T cells, while CD8⁺ T cells specific for epitopes NP205 and GP118 were detected by IFN-γ staining following peptide stimulation.

FIG. 12A is a series of FACS plots showing phenotypic changes (expression of CD127, CD62L, KLRG-1 and Bcl-2) of virus-specific CD8⁺ T cells obtained from the spleen of untreated and rapamycin-treated mice on Day 35 post-infection. FIG. 12B is a series of FACS plots showing the percentage of virus-specific CD8⁺ T cells co-expressing CD127 and either CD62L or KLRG-1. FIG. 12C is a series of graphs showing the kinetics of phenotypic changes of DbGP33 tetramer-positive LCMV-specific CD8⁺ T cells in PBMC obtained from untreated and rapamycin-treated mice at intervals from Day 0 to Day 30.

FIG. 13A is a schematic of the experimental design to demonstrate that low dose rapamycin treatment induces high quality memory T cells during recall responses. Thy-1.1⁺ P14 memory T cells were adoptively transferred into Thy-1.2⁺ recipient mice and low dose rapamycin treatment was initiated on the same day (Day −1). The following day (Day 0), recipient mice were infected with LCMV. FIG. 13B is a series of FACS plots showing LCMV-specific CD8⁺ T cell responses after infection. Shown is the percentage of Thy-1.1⁺ P14 cells in PBMCs obtained from untreated and rapamycin-treated mice on Days 8, 14, 22 and 35 post-infection. FIG. 13C is a series of FACS plots showing the percentage of LCMV-specific CD8⁺ T cells expressing CD62L and CD127 on Days 8, 14, 22 and 35 post-infection.

FIG. 14A is a schematic of the experimental design to demonstrate that low dose rapamycin treatment induces high quality memory T cells upon immunization with virus-like particles (VLPs). Rapamycin treatment was initiated one day prior to immunization with VLPs. FIG. 14B is a graph showing DbGP33 tetramer-positive CD8⁺ T cell responses in PBMCs obtained from untreated and rapamycin-treated mice. FIG. 14C is a graph showing the number of DbGP33 tetramer-positive CD8⁺ T cells obtained from the spleen of untreated and rapamycin-treated mice on Day 34 post-infection. FIGS. 14D and 14E are FACS plots showing the phenotypic analysis of DbGP33 tetramer-positive CD8⁺ T cells in the spleen on Day 34 post-immunization.

FIG. 15 is a schematic depiction of the mammalian target of rapamycin (mTOR) pathway. mTOR is part of two distinct complexes, mTOR complex 1 (mTORC1) and complex 2 (mTORC2). mTORC1 is sensitive to rapamycin.

FIG. 16A is a schematic of the experimental design for raptor knockdown in virus-specific CD8⁺ T cells. Retrovirus encoding a control or raptor-specific short hairpin RNA (shRNA) (RNAi) was constructed and used to transduce LCMV-specific P14 cells. Transduced P14 cells were adoptively transferred into naïve mice, and the mice were then infected with LCMV. FIG. 16B is a series of graphs showing the phenotypic changes of adoptively transferred P14 cells obtained from the spleen on Day 35 after LCMV infection. GFP-positive cells are retrovirus-transduced cells.

FIG. 17A is a schematic of the experimental design to demonstrate that LCMV-specific CD8⁺ T cells become rapamycin sensitive after FKBP12 knockdown. Control or FKBP12 RNAi retrovirus transduced LCMV-specific P14 cells were adoptively transferred into naïve mice and the mice were infected with LCMV. Rapamycin treatment was initiated on the day prior to LCMV infection (Day −1). FIG. 17B is a series of graphs showing the phenotypic changes of adoptively transferred P14 cells on Day 16 post-LCMV infection in PBMC. Green fluorescent protein (GFP)-positive cells are retrovirus-transduced cells.

FIG. 18 shows FACS plots demonstrating that low dose rapamycin treatment enhances the number of virus-specific memory CD4⁺ T cells. Rapamycin treatment was initiated one day prior to infection with LCMV. Spleen cells were stimulated with LCMV GP61 peptide specific for CD4⁺ T cells and intracellular cytokine staining was performed. The percentage of CD4⁺ T cells expressing IL-2 and/or IFN-γ in the presence and absence of peptide stimulation is indicated.

FIG. 19A is a schematic of the experimental design to demonstrate that low dose rapamycin treatment improves the quantity and quality of memory T cells induced by recombinant adenovirus serotype 5 (rAd5) that expresses LCMV glycoprotein (rAd5-LCMV-GP). Rapamycin treatment was initiated one day prior to vaccination with rAd5-LCMV-GP. FIG. 19B is a graph showing the number of DbGP33 tetramer-positive CD8⁺ T cells in the spleen on Day 35 post-vaccination. FIG. 19C is a series of FACS plots showing phenotypic analysis of DbGP33 tetramer-positive CD8⁺ T cells in the spleen on Day 35 post-vaccination.

FIG. 20A is a graph showing the kinetics of endogenous GP33 epitope-specific CD8⁺ T cells in PBMCs of LCMV-infected B6 mice treated with rapamycin from Day −1 to Day 30 post-infection (shaded area) (No Rapa, n=3 mice; Rapa Tx, n=6). FIG. 20B is a series of FACS plots showing phenotypic analysis of endogenous DbGP33 tetramer-positive cells in the spleen at Day 36 post infection. FIG. 20C is schematic diagram and pair of FACS plots showing GP33 epitope-specific P14 transgenic memory CD8⁺ T cells (Day 34 post-infection) were generated in the presence or absence of rapamycin, labeled with CFSE and then adoptively transferred into naïve mice to monitor their homeostatic proliferation. CFSE dilution of P14 cells at 30 days post transfer is shown in the FACS plots and the number represents percentage of memory cells that divided more than two times. FIG. 20D is a schematic diagram and a pair of graphs showing that memory P14 cells derived from rapamycin-treated or untreated mice were adoptively transferred and mice were challenged with vaccinia virus expressing the GP33 epitope (VVGP33). Kinetics of P14 cells in PBMCs after challenge (left graph) and the total P14 cell numbers in spleen on Day 30 post-infection (right graph) are shown (No Rapa, n=4; Rapa Tx, n=6). Error bars indicate standard error of the mean (SEM).

FIG. 21A is a graph showing kinetics of endogenous GP33 epitope-specific CD8⁺ T cells in PBMCs of LCMV-infected B6 mice treated with rapamycin from Day −1 to Day 8 post-infection (shaded area) (n=3-6 for each time point). FIG. 21B is a graph showing the average number of DbGP33 tetramer-positive cells on Day 36 post-infection in spleens of LCMV-infected mice treated with rapamycin (No Rapa, n=9; Rapa Tx Day −1 to Day 8, n=3). FIG. 21C is a series of FACS plots showing CD127, KLRG-1, and Bcl-2 expression on endogenous DbGP33 tetramer-positive cells in PBMCs at 8 days post-LCMV infection in B6 mice. Rapamycin was administered from Day −1 to Day 8 post-infection. FIG. 21D is a series of FACS plots showing phenotypic analysis of DbGP33 tetramer-positive cells in spleens of LCMV-infected mice (rapamycin treatment from Day −1 to Day 8 post-infection). Error bars indicate SEM.

FIG. 22A is a graph showing kinetics of endogenous GP33 epitope-specific CD8⁺ T cells in PBMCs of LCMV-infected B6 mice treated with rapamycin from Day 8 to Day 36 post-infection (shaded area) (No Rapa, n=9 mice; Rapa Tx, n=9). FIG. 22B is a series of graphs showing phenotypic changes in endogenous DbGP33 tetramer-positive CD8⁺ T cells in the spleen on Day 36 post-LCMV infection (n=12 for each group). B6 Mice were treated with rapamycin during the effector to memory T cell transition period (Days 8-35 post-infection). FIG. 22C is a pair of FACS plots and a schematic diagram showing CD62L-negative Day 8 P14 transgenic effector CD8⁺ T cells were purified, labeled with CFSE, and then adoptively transferred into naïve mice. Half of these mice were treated with rapamycin after transfer and CD62L conversion in the antigen-specific CD8⁺ T cells was analyzed longitudinally in the blood (FIG. 22D). FIG. 22E is a series of FACS plots showing CFSE profile and CD62L expression on antigen-specific memory CD8⁺ T cells in the spleen at Day 27 after transfer of CD62L-negative effector T cells. FIG. 22F is a schematic diagram showing CD62L-negative Day 8 P14 transgenic effector CD8⁺ T cells were adoptively transferred into naïve mice. These mice were treated with rapamycin for 25 days, and were challenged with VVGP33 on Day 28 post-transfer. At 5 days after challenge, P14 expansion in spleen (FIG. 22G) and viral titers in ovary (FIG. 22H) were analyzed (n=4-6 for each group). Flow data were gated on CD8⁺ T cells. Error bars indicate SEM.

FIGS. 23A-23C are graphs showing knockdown of specific genes using a retrovirus based RNAi system. Retrovirus-transduced LCMV-specific P14 transgenic CD8⁺ T cells (marked by GFP expression) were adoptively transferred into naïve mice, followed by LCMV infection. Phenotypic analysis of retrovirus transduced cells (GFP⁺) and non-transduced (GFP⁻) P14 cells in PBMCs was performed on Days 14-16 post infection. FIGS. 23A and 23B are a series of graphs showing changes in expression of phenotypic markers following mTOR (A) or raptor (B) RNAi treatment. Each line shows expression of the indicated phenotypic markers on transduced and non-transduced antigen-specific CD8⁺ T cells in individual animals. The same control data are shown in A and B. FIG. 23C is a series of graphs showing changes in expression of phenotypic markers following FKBP12 RNAi treatment. FKBP12 RNAi expressing retrovirus- or control retrovirus-transduced P14 transgenic CD8⁺ T cells (marked by GFP expression) were adoptively transferred into naïve mice, followed by LCMV infection. Half of the mice were treated with rapamycin throughout infection. Phenotypic analysis of retrovirus-transduced cells (GFP⁺) and non-transduced (GFP⁻) P14 cells in the PBMCs was performed on Days 14-16 post-infection.

FIG. 24A is a schematic diagram showing LCMV-specific P14 transgenic memory CD8⁺ T cells (Thy-1.1) were adoptively transferred into Thy-1.2 naïve mice and these mice were infected with LCMV in the presence or absence of rapamycin (Day −1 to Day 32 post-infection). FIG. 24B is a graph showing kinetics of P14 recall responses upon infection. Flow data are gated on lymphocytes in PBMCs. FIGS. 24C and 24D are a pair of graphs showing CD127 expression and CD62L expression, respectively, on P14 cells during recall responses. Error bars and shaded area indicate SEM and rapamycin treatment, respectively.

FIGS. 25A-25C demonstrate that mTOR regulates memory CD8⁺ T cell responses in non-human primates. Rhesus macaques were vaccinated with MVA (booster immunization) in the presence or absence of rapamycin (n=3 for each group). PBMCs from vaccinated macaques were stimulated with vaccinia virus and analyzed for IFN-γ production. FIG. 25A is a series of FACS plots analyzing IFN-γ production from representative macaques (gated on CD3⁺CD8⁺ cells). FIG. 25B is a graph showing kinetics of IFN-γ producing vaccinia virus-specific CD8⁺ T cells in individual animals. The shaded area shows rapamycin treatment. FIG. 25C is a graph showing IFN-γ producing vaccinia virus-specific CD8⁺ T cell contraction rate over time. The number of vaccinia virus-specific CD8⁺ T cells at the peak between days 7-21 post-vaccination was taken as 100% for individual animals, and contraction rate was calculated as a percentage of this peak response. Lines and shaded area show nonlinear regression (one phase exponential decay) and rapamycin treatment, respectively.

SEQUENCE LISTING

The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. For double-stranded DNA sequences, only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. In the accompanying sequence listing:

SEQ ID NO: 1 is the nucleotide sequence of a shRNA specific for raptor.

SEQ ID NO: 2 is the nucleotide sequence of a shRNA specific for FKBP12.

SEQ ID NOs: 3 and 4 are the nucleotide and amino acid sequences, respectively, of human mTOR deposited under GENBANK™ Accession No. NM_004958 on Apr. 4, 2002.

SEQ ID NOs: 5 and 6 are the nucleotide and amino acid sequences, respectively, of human mTOR deposited under GENBANK™ Accession No. BC117166 on Jun. 26, 2006.

SEQ ID NOs: 7 and 8 are the nucleotide and amino acid sequences, respectively, of LCMV glycoprotein deposited under GENBANK™ Accession No. M20869 on Aug. 2, 1993.

SEQ ID NO: 9 is the amino acid sequence of the LCMV gp33-41 epitope.

SEQ ID NOs: 10 and 11 are the nucleotide sequences of the sense and antisense strands, respectively, of an mTOR-specific shRNA.

SEQ ID NOs: 12 and 13 are the nucleotide sequences of the sense and antisense strands, respectively, of a raptor-specific shRNA.

SEQ ID NOs: 14 and 15 are the nucleotide sequences of the sense and antisense strands, respectively, of a FKBP12-specific shRNA.

SEQ ID NOs: 16 and 17 are the nucleotide sequences of the sense and antisense strands, respectively, of an S6K1-specific shRNA.

SEQ ID NOs: 18 and 19 are the nucleotide sequences of the sense and antisense strands, respectively, of an eIF4E-specific shRNA.

DETAILED DESCRIPTION I. Abbreviations

Ad Adenovirus

AFP Alphafetoprotein

CD Cluster of differentiation

CEA Carcinoembryonic antigen

CFSE Carboxyfluorescein succinimidyl ester

DC Dendritic cell

FACS Fluorescence activated cell sorting

FBS Fetal bovine serum

FKBP12 FK506-binding protein 12

GβL G-protein β-subunit

GFP Green fluorescent protein

GP Glycoprotein

HBV Hepatitis B virus

HBcAg Hepatitis B core antigen

HCV Hepatitis C virus

HIV Human immunodeficiency virus

HPV Human papillomavirus

IFN Interferon

IGF Insulin growth factor

IP Intraperitoneally

KLRG Killer cell lectin-like receptor G

LCMV Lymphocytic choriomeningitis virus

LN Lymph node

MHC Major histocompatibility complex

miRNA Micro RNA

mTOR Mammalian target of rapamycin

mTORC1 mTOR complex 1

mTORC2 mTOR complex 2

MVA Modified Vaccinia Ankara

NP Nucleoprotein

ODN Oligodeoxynucleotide

PBMC Peripheral blood mononuclear cell

PFU Plaque forming unit

PRAME Preferentially expressed antigen of melanoma

PrCP Peridinin chlorophyll protein

PSA Prostate specific antigen

Raptor Regulatory associated protein of mTOR

Rictor Rapamycin-insensitive companion of mTOR

RNA Ribonucleic acid

RNAi RNA interference

SEM Standard error of the mean

shRNA Short hairpin RNA

VLP Virus-like particle

VV Vaccinia virus

WT Wilms tumor

II. Terms and Methods

Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).

In order to facilitate review of the various embodiments of the disclosure, the following explanations of specific terms are provided:

Acute infection: An infection (such as a viral infection) having a relatively short time course.

Adjuvant: A substance or vehicle that non-specifically enhances the immune response to an antigen. Adjuvants can include a suspension of minerals (alum, aluminum hydroxide, or phosphate) on which antigen is adsorbed; or water-in-oil emulsion in which antigen solution is emulsified in mineral oil (for example, Freund's incomplete adjuvant), sometimes with the inclusion of killed mycobacteria (Freund's complete adjuvant) to further enhance antigenicity. Immunostimulatory oligonucleotides (such as those including a CpG motif) can also be used as adjuvants (for example, see U.S. Pat. Nos. 6,194,388; 6,207,646; 6,214,806; 6,218,371; 6,239,116; 6,339,068; 6,406,705; and 6,429,199). Adjuvants also include biological molecules, such as costimulatory molecules. Exemplary biological adjuvants include IL-2, RANTES, GM-CSF, TNF-α, IFN-γ, G-CSF, LFA-3, CD72, B7-1, B7-2, OX-40L and 41 BBL.

Administration: The introduction of a composition into a subject by a chosen route. For example, if the chosen route is intravenous, the composition (for example, rapamycin) is administered by introducing the composition into a vein of the subject.

Animal: Living multi-cellular vertebrate organisms, a category that includes, for example, mammals and birds. The term mammal includes both human and non-human mammals. Similarly, the term “subject” includes both human and veterinary subjects.

Antibody: A polypeptide ligand comprising at least a light chain or heavy chain immunoglobulin variable region which specifically recognizes and binds an epitope of an antigen. Antibodies are composed of a heavy and a light chain, each of which has a variable region, termed the variable heavy (V_(H)) region and the variable light (V_(L)) region. Together, the V_(H) region and the V_(L) region are responsible for binding the antigen recognized by the antibody.

Antibodies include intact immunoglobulins and the variants and portions of antibodies well known in the art, such as Fab fragments, Fab′ fragments, F(ab)′₂ fragments, single chain Fv proteins (“scFv”), and disulfide stabilized Fv proteins (“dsFv”). A scFv protein is a fusion protein in which a light chain variable region of an immunoglobulin and a heavy chain variable region of an immunoglobulin are bound by a linker, while in dsFvs, the chains have been mutated to introduce a disulfide bond to stabilize the association of the chains. The term also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies), heteroconjugate antibodies (such as, bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology, 3^(rd) Ed., W. H. Freeman & Co., New York, 1997.

Typically, a naturally occurring immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. There are two types of light chain, lambda (λ) and kappa (k). There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE.

Each heavy and light chain contains a constant region and a variable region, (the regions are also known as “domains”). In combination, the heavy and the light chain variable regions specifically bind the antigen. Light and heavy chain variable regions contain a “framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or “CDRs.” The extent of the framework region and CDRs have been defined (see, Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991). The Kabat database is now maintained online. The sequences of the framework regions of different light or heavy chains are relatively conserved within a species, such as humans. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space.

The CDRs are primarily responsible for binding to an epitope of an antigen. The CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also typically identified by the chain in which the particular CDR is located. Thus, a V_(H) CDR3 is located in the variable domain of the heavy chain of the antibody in which it is found, whereas a V_(L) CDR1 is the CDR1 from the variable domain of the light chain of the antibody in which it is found. Antibodies with different specificities (i.e. different combining sites for different antigens) have different CDRs. Although it is the CDRs that vary from antibody to antibody, only a limited number of amino acid positions within the CDRs are directly involved in antigen binding. These positions within the CDRs are called specificity determining residues (SDRs).

References to “V_(H)” or “VH” refer to the variable region of an immunoglobulin heavy chain, including that of an Fv, scFv, dsFv or Fab. References to “V_(L)” or “VL” refer to the variable region of an immunoglobulin light chain, including that of an Fv, scFv, dsFv or Fab.

Antigen: A compound, composition, or substance that can stimulate the production of antibodies or a T-cell response in an animal, including compositions that are injected or absorbed into an animal. An antigen reacts with the products of specific humoral or cellular immunity, including those induced by heterologous immunogens.

Antigen-specific T cell response: Refers to a T cell immune response that is directed against a particular antigen. Antigen-specific T cells are T cells that are capable of specifically recognizing (via T cell receptors) and responding to an antigen. As used herein, “enhancing” an antigen-specific T cell response includes, but is not limited to, increasing the number, quality and/or activity of T cells, such as CD4⁺ and/or CD8⁺ memory T cells. There are three phases of an antigen-specific CD8⁺ T cell response after exposure to antigen (such as during a viral infection). First, during the expansion phase naïve antigen-specific CD8⁺ T cells exponentially expand and become effector T cells. These effector T cells stop proliferating approximately 1 to 2 weeks after exposure and enter the contraction phase. During the contraction phase, effector CD8⁺ T cells gradually acquire memory T cell phenotype and function. The contraction phase is also referred to as the “cell death phase” as a significant number of activated T cells (often about 90%) die during this phase. The maintenance phase, which is also referred to as the “memory phase,” follows the contraction phase and is characterized by long-term survival of antigen-specific memory cells.

Antisense oligonucleotide: As used herein, an “antisense oligonucleotide” is a single-stranded antisense compound that is a nucleic acid-based oligomer. An antisense oligonucleotide can include one or more chemical modifications to the sugar, base, and/or internucleoside linkages. Generally, antisense oligonucleotides are “DNA-like” such that when the antisense oligonucleotide hybridizes to a target mRNA, the duplex is recognized by RNase H (an enzyme that recognizes DNA:RNA duplexes), resulting in cleavage of the mRNA.

Binding affinity: Affinity of an antibody for an antigen. In one embodiment, affinity is calculated by a modification of the Scatchard method described by Frankel et al. (Mol. Immunol., 16:101-106, 1979). In some cases, binding affinity is measured by an antigen/antibody dissociation rate. In another cases, a high binding affinity is measured by a competition radioimmunoassay or ELISA.

CD8⁺ effector T cells/CD4⁺ effector T cells: Activated T cells that express CD8 or CD4, respectively. During an immune response, effector T cells divide rapidly and secrete cytokines to modulate the immune response. T effector cells are also known as T helper cells.

CD8⁺ memory T cells/CD4⁺ memory T cells: Antigen-specific CD8⁺ or CD4⁺ T cells that persist long-term after an immune response. Upon re-exposure to the antigen, memory T cells expand and become T effector cells.

Chronic infection: An infection (such as a viral infection) that persists for a relatively long period of time. Chronic infections typically result in little to no change in symptoms over time and/or progress very slowly.

High quality T cells: As used herein, a “high quality T cell” is an antigen-specific T cell that exhibits superior properties relative to standard T cells, such as increased proliferation in response to antigen or increased viral clearance. High quality T cells can be identified by detecting the expression level of specific cell-surface markers. In some embodiments, a high quality T cell is a T cell expressing one or more of CD127^(high), CD62L^(high), KLRG-1^(low), CD27^(high) and Bcl-2^(high). In some embodiments, high quality T cells are CD127^(high), CD27^(high) and Bcl-2^(high). In some embodiments, high quality T cells are KLRG-1^(low), CD27^(high) and Bcl-2^(high). In some embodiments, high quality T cells are CD127^(high), CD62L^(high), KLRG-1^(low) and Bcl-2^(high). In some embodiments, high quality T cells are CD127^(high), CD62L^(high) and KLRG-1^(low). Similarly, “enhancing the quality of a T cell” refers to increasing functional activity of a T cell, such as increased proliferation in response to antigen or increased viral clearance. In some embodiments, enhancing the quality of a T cell includes increasing expression of one or more of CD127, CD62L, CD27 and Bcl-2, and/or decreasing expression of KLRG-1. In some embodiments, the increase or decrease in expression is about 1.5-fold, about 2-fold, about 3-fold, about 5-fold or about 10-fold. High quality T cells can be identified according to standard methods known in the art, such as by FACS.

Immune response: A response of a cell of the immune system, such as a B cell or T cell, to a stimulus. In some embodiments, the response is specific for a particular antigen (an “antigen-specific response”). In some embodiments, an immune response is a T cell response, such as a CD8⁺ response. In another embodiment, the response is a B cell response, and results in the production of antigen-specific antibodies. As used herein, “stimulating an immune response” refers to promoting or enhancing the response of the cells of the immune system to a stimulus, such as an antigen.

Immunogen: A compound, composition, or substance which is capable, under appropriate conditions, of stimulating an immune response, such as the production of antibodies or a T-cell response in an animal, including compositions that are injected or absorbed into an animal.

Increasing the proportion of CD127^(High)KLRG-1^(Low) CD8⁺ T cells: As used herein, “increasing the proportion of CD127^(High)KLRG-1^(Low) CD8⁺ T cells” refers to increasing the ratio of CD127^(High)KLRG-1^(Low) to CD127^(Low)KLRG-1^(High) CD8⁺ T cells in the subject exposed to an antigen (such as an infectious agent, tumor or vaccine). As described herein, day 8 (the end of the T cell expansion phase) effector CD8⁺ T cell populations are characterized by two subsets: (1) terminal effector T cells (CD127^(Low)KLRG-1^(High)) a large percentage of which die over the following 2-4 weeks; and (2) memory precursor cells (CD127^(High)KLRG-1^(Low)) which survive and differentiate to produce long-lived memory T cells. As disclosed herein, treatment of a subject exposed to an antigen with an mTOR inhibitor increases the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells in the subject. T cells expressing CD127 and KLRG-1, and their relative expression levels, can be identified according to standard methods known in the art, such as by FACS.

Inhibit expression or activity: As used herein, a compound that inhibits expression or activity of mTOR is a compound that reduces the level of mTOR mRNA or protein in a cell or tissue, or reduces (including eliminates) one or more activities of mTOR. For example, an antisense compound targeting mTOR inhibits expression of mTOR by promoting the degradation of mTOR mRNA, thereby reducing the level of mTOR protein. In some embodiments, mTOR expression is inhibited at least 10%, at least 25%, at least 50%, at least 75%, at least 90%, or at least 95% relative to a control, such as untreated control cells. As another example, an antibody or small molecule that specifically binds or targets mTOR may inhibit activity of mTOR by directly inhibiting its kinase activity or by preventing mTOR protein from interacting with another protein. In some embodiments, mTOR activity is inhibited at least 10%, at least 25%, at least 50%, at least 75%, at least 90%, or at least 95% relative to an untreated control.

Isolated: An “isolated” biological component, such as a nucleic acid, protein (including antibodies) or organelle that has been substantially separated or purified away from other biological components in the environment (such as a cell) in which the component naturally occurs, i.e., other chromosomal and extra-chromosomal DNA and RNA, proteins and organelles. Nucleic acids and proteins that have been “isolated” include nucleic acids and proteins purified by standard purification methods. The term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.

Low dose rapamycin: Refers to a dose of rapamycin that does not suppress antigen-specific T cell immune responses when administered during the expansion, contraction or maintenance phases of a T cell response. Generally, a low dose of rapamycin is about 0.01 to about 0.15 mg/kg, such as about 0.05 to about 0.1, or a dose that results in a blood concentration of approximately 5 to 20 ng/ml. In some examples a low dose of rapamycin is about 0.01, about 0.02, about 0.03, about 0.04, about 0.05, about 0.06, about 0.07, about 0.08, about 0.09, about 0.10, about 0.11, about 0.12, about 0.13, about 0.14 or about 0.15 mg/kg. In this context, “about” refers to a value within 0.005 mg/kg.

MicroRNA (miRNA): Single-stranded RNA molecules that regulate gene expression. miRNAs are generally 21-23 nucleotides in length. miRNAs are processed from primary transcripts known as pri-miRNA to short stem-loop structures called pre-miRNA and finally to functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA molecules, and their primary function is to down-regulate gene expression. MicroRNAs regulate gene expression through the RNAi pathway.

mTOR: A serine/threonine kinase that regulates the expression of proteins involved in cell growth and proliferation via phosphorylation of specific substrates. As such, mTOR plays an integral role in the response to numerous hormones and growth factors. Synonyms for mTOR include FRAP1, FKBP12-rapamycin complex-associated protein, FK506-binding protein 12-rapamycin complex-associated protein 1, rapamycin target protein and RAPT1. Nucleotide and amino acid sequences of mTOR are known in the art (for example, GENBANK™ Accession No. NM_004958, deposited on Apr. 4, 2002 (SEQ ID NOs: 3 and 4), and GENBANK™ Accession No. BC117166, deposited on Jun. 26, 2006 (SEQ ID NOs: 5 and 6)).

mTOR inhibitor: A molecule that inhibits expression or activity of mTOR. mTOR inhibitors include, but are not limited to small molecule, antibody, peptide and nucleic acid inhibitors. For example, an mTOR inhibitor can be a molecule that inhibits the kinase activity of mTOR or inhibits binding of mTOR to a ligand. Inhibitors of mTOR also include molecules that down-regulate expression of mTOR, such as an antisense compound. A number of mTOR inhibitors are known in the art and are discussed below. In some embodiments, the mTOR inhibitor is rapamycin or a rapamycin analog.

Pathogen: A biological agent that causes disease or illness to its host. Pathogens include, for example, bacteria, viruses, fungi, protozoa and parasites. Pathogens are also referred to as infectious agents or infectious microorganisms.

Examples of pathogenic viruses include, but are not limited to those in the following virus families: Retroviridae (for example, human immunodeficiency virus (HIV), human T-cell leukemia viruses; Picornaviridae (for example, polio virus, hepatitis A virus, hepatitis C virus, enteroviruses, human coxsackie viruses, rhinoviruses, echoviruses, foot-and-mouth disease virus); Caliciviridae (such as strains that cause gastroenteritis, including Norwalk virus); Togaviridae (for example, alphaviruses (including chikungunya virus, equine encephalitis viruses, Simliki Forest virus, Sindbis virus, Ross River virus), rubella viruses); Flaviridae (for example, dengue viruses, yellow fever viruses, West Nile virus, St. Louis encephalitis virus, Japanese encephalitis virus, Powassan virus and other encephalitis viruses); Coronaviridae (for example, coronaviruses, severe acute respiratory syndrome (SARS) virus; Rhabdoviridae (for example, vesicular stomatitis viruses, rabies viruses); Filoviridae (for example, Ebola virus, Marburg virus); Paramyxoviridae (for example, parainfluenza viruses, mumps virus, measles virus, respiratory syncytial virus); Orthomyxoviridae (for example, influenza viruses, including avian flu and swine flu); Bunyaviridae (for example, Hantaan viruses, Sin Nombre virus, Rift Valley fever virus, bunya viruses, phleboviruses and Nairo viruses); Arenaviridae (such as Lassa fever virus and other hemorrhagic fever viruses, Machupo virus, Junin virus); Reoviridae (e.g., reoviruses, orbiviurses, rotaviruses); Birnaviridae; Hepadnaviridae (hepatitis B virus); Parvoviridae (parvoviruses); Papovaviridae (papilloma viruses, polyoma viruses, BK-virus); Adenoviridae (adenoviruses); Herpesviridae (herpes simplex virus (HSV)-1 and HSV-2; cytomegalovirus; Epstein-Barr virus; varicella zoster virus; and other herpes viruses, including HSV-6); Poxviridae (variola viruses, vaccinia viruses, pox viruses); and Iridoviridae (such as African swine fever virus); Astroviridae; and unclassified viruses (for example, the etiological agents of spongiform encephalopathies, the agent of delta hepatitis (thought to be a defective satellite of hepatitis B virus).

Examples of bacterial pathogens include, but are not limited to: Helicobacter pylori, Escherichia coli, Vibrio cholerae, Borelia burgdorferi, Legionella pneumophilia, Mycobacteria sps (such as. M. tuberculosis, M. avium, M. intracellulare, M. kansaii, M. gordonae), Staphylococcus aureus, Neisseria gonorrhoeae, Neisseria meningitidis, Listeria monocytogenes, Streptococcus pyogenes (Group A Streptococcus), Streptococcus agalactiae (Group B Streptococcus), Streptococcus (viridans group), Streptococcus faecalis, Streptococcus bovis, Streptococcus (anaerobic sps.), Streptococcus pneumoniae, pathogenic Campylobacter sp., Enterococcus sp., Haemophilus influenzae, Bacillus anthracis, corynebacterium diphtherias, corynebacterium sp., Erysipelothrix rhusiopathiae, Clostridium perfringens, Clostridium tetani, Enterobacter aerogenes, Klebsiella pneumoniae, Pasteurella multocida, Bacteroides sp., Fusobacterium nucleatum, Streptobacillus moniliformis, Treponema pallidium, Treponema pertenue, Leptospira, Bordetella pertussis, Shigella flexnerii, Shigella dysenteriae and Actinomyces israelli.

Examples of fungal pathogens include, but are not limited to: Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Candida albicans.

Other pathogens (such as parasitic pathogens) include, but are not limited to: Plasmodium falciparum, Plasmodium vivax, Trypanosoma cruzi and Toxoplasma gondii.

Pharmaceutical agent: A chemical compound or composition capable of inducing a desired therapeutic or prophylactic effect when properly administered to a subject or a cell.

Pharmaceutically acceptable carriers: The pharmaceutically acceptable carriers of use are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 15th Edition, 1975, describes compositions and formulations suitable for pharmaceutical delivery of the compositions disclosed herein.

In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (such as powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.

Polypeptide: A polymer in which the monomers are amino acid residues that are joined together through amide bonds. When the amino acids are alpha-amino acids, either the L-optical isomer or the D-optical isomer can be used, the L-isomers being preferred. The term polypeptide or protein as used herein encompasses any amino acid sequence and includes modified sequences such as glycoproteins. The term polypeptide is specifically intended to cover naturally occurring proteins, as well as those that are recombinantly or synthetically produced.

The term polypeptide fragment refers to a portion of a polypeptide that exhibits at least one useful epitope. The phrase “functional fragment(s) of a polypeptide” refers to all fragments of a polypeptide that retain an activity, or a measurable portion of an activity, of the polypeptide from which the fragment is derived. Fragments, for example, can vary in size from a polypeptide fragment as small as an epitope capable of binding an antibody molecule to a large polypeptide capable of participating in the characteristic induction or programming of phenotypic changes within a cell. An epitope is a region of a polypeptide capable of binding an immunoglobulin generated in response to contact with an antigen. Thus, smaller peptides containing the biological activity of insulin, or conservative variants of the insulin, are thus included as being of use.

Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that are considered to be conservative substitutions for one another:

1) Alanine (A), Serine (S), Threonine (T);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

In some circumstances, variations in the cDNA sequence that result in amino acid changes, whether conservative or not, are minimized in order to preserve the functional and immunologic identity of the encoded protein. The immunologic identity of the protein may be assessed by determining whether it is recognized by an antibody; a variant that is recognized by such an antibody is immunologically conserved. Any cDNA sequence variant will preferably introduce no more than twenty, and preferably fewer than ten amino acid substitutions into the encoded polypeptide. Variant amino acid sequences may, for example, be 80%, 90%, or even 95% or 98% identical to the native amino acid sequence. Programs and algorithms for determining percentage identity can be found at the National Center for Biotechnology Information web site.

Preventing, treating or ameliorating a disease: “Preventing” a disease refers to inhibiting the full development of a disease. “Treating” refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition after it has begun to develop. “Ameliorating” refers to the reduction in the number or severity of signs or symptoms of a disease.

Purified: The term purified does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified antigen is one in which the specified antigen is more enriched than it is in its generative environment, for instance within a cell extract. Preferably, a preparation of a specified antigen is purified such that the antigen represents at least 75% of the total content of the preparation. In some embodiments, a purified preparation contains at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more of the specified antigen. As used herein, “purified” antigens include recombinantly produced antigens.

Rapamycin: A small molecule with known immunosuppressive and anti-proliferative properties. Rapamycin, also known as sirolimus, is a macrolide that was first discovered as a product of the bacterium Streptomyces hygroscopicus. Rapamycin binds and inhibits the activity of mTOR. The chemical formula of rapamycin is C₅₁H₇₉NO₁₃ and the International Union of Pure and Applied Chemistry (IUPAC) name is (3S,6R,7E,9R,10R,12R,14S,15E,17E,19E,21S,23S,26R,27R,34aS)-9,10,12,13,14,21,22,23,24,25,26,27,32,33,34,34a-hexadecahydro-9,27-dihydroxy-3-[(1R)-2-[(1S,3R,4R)-4-hydroxy-3-methoxycyclohexyl]-1-methylethyl]-10,21-dimethoxy-6, 8,12,14,20,26-hexamethyl-23,27-epoxy-3H-pyrido[2,1-c][1,4]-oxaazacyclohentriacontine-1,5,11,28,29(4H,6H,31H)-pentone.

Ribozyme: A catalytic RNA molecule. In some cases, ribozymes can bind to specific sites on other RNA molecules and catalyze the hydrolysis of phosphodiester bonds in the RNA molecules.

RNA interference (RNAi): Refers to a cellular process that inhibits expression of genes, including cellular and viral genes. RNAi is a form of antisense-mediated gene silencing involving the introduction of double stranded RNA-like oligonucleotides leading to the sequence-specific reduction of RNA transcripts. Double-stranded RNA molecules that inhibit gene expression through the RNAi pathway include siRNAs, miRNAs, and shRNAs.

Sample: As used herein, a “sample” obtained from a subject refers to a cell, fluid or tissue sample. Bodily fluids include, but are not limited to, blood, serum, urine, saliva and spinal fluid. Cell samples include, for example, PBMCs, white blood cells, lymphocytes, or other cells of the immune system.

Short hairpin RNA (shRNA): A sequence of RNA that makes a tight hairpin turn and can be used to silence gene expression via the RNAi pathway. The shRNA hairpin structure is cleaved by the cellular machinery into siRNA.

Small interfering RNA (siRNA): A double-stranded nucleic acid molecule that modulates gene expression through the RNAi pathway. siRNA molecules are generally 20-25 nucleotides in length with 2-nucleotide overhangs on each 3′ end. However, siRNAs can also be blunt ended. Generally, one strand of a siRNA molecule is at least partially complementary to a target nucleic acid, such as a target mRNA. siRNAs are also referred to as “small inhibitory RNAs.”

Small molecule inhibitor: A molecule, typically with a molecular weight less than about 1000 Daltons, or in some embodiments, less than about 500 Daltons, wherein the molecule is capable of inhibiting, to some measurable extent, an activity of a target molecule.

Subject: Living multi-cellular vertebrate organisms, a category that includes both human and veterinary subjects, including human and non-human mammals.

Therapeutically effective amount: A quantity of a specific substance sufficient to achieve a desired effect in a subject being treated. For instance, this can be the amount of an mTOR inhibitor necessary to enhance a T cell response.

Tumor antigen: A tumor antigen is an antigen produced by tumor cells that can stimulate tumor-specific T-cell immune responses. Exemplary tumor antigens include, but are not limited to, RAGE-1, tyrosinase, MAGE-1, MAGE-2, NY-ESO-1, Melan-A/MART-1, glycoprotein (gp) 75, gp100, beta-catenin, preferentially expressed antigen of melanoma (PRAME), MUM-1, Wilms tumor (WT)-1, carcinoembryonic antigen (CEA), and PR-1. Additional tumor antigens are known in the art (for example see Novellino et al., Cancer Immunol. Immunother. 54(3):187-207, 2005) and are described below. Tumor antigens are also referred to as “cancer antigens.”

Tumor, cancer, neoplasia or malignancy: The result of abnormal and uncontrolled growth of cells. Neoplasia, malignancy, cancer and tumor are often used interchangeably and refer to abnormal growth of a tissue or cells that results from excessive cell division. Hematological cancers are cancers of the blood or bone marrow. Examples of hematological tumors include leukemias, including acute leukemias (such as acute lymphocytic leukemia, acute myelocytic leukemia, acute myelogenous leukemia and myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia), chronic leukemias (such as chronic myelocytic (granulocytic) leukemia, chronic myelogenous leukemia, and chronic lymphocytic leukemia), polycythemia vera, lymphoma, Hodgkin's disease, non-Hodgkin's lymphoma (indolent and high grade forms), multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease, myelodysplastic syndrome, hairy cell leukemia and myelodysplasia.

Solid tumors are abnormal masses of tissue that usually do not contain cysts or liquid areas and are named for the type of cells that form them. Examples of solid tumors, such as sarcomas and carcinomas, include fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, and other sarcomas, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, lymphoid malignancy, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer, hepatocellular carcinoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, medullary thyroid carcinoma, papillary thyroid carcinoma, pheochromocytomas sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, Wilms' tumor, cervical cancer, testicular tumor, seminoma, bladder carcinoma, melanoma, and CNS tumors (such as a glioma, astrocytoma, medulloblastoma, craniopharyogioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, neuroblastoma and retinoblastoma).

Vaccine: A preparation of immunogenic material capable of stimulating an immune response, administered for the prevention, amelioration, or treatment of infectious or other types of disease, such as cancer. The immunogenic material may include live-attenuated or killed microorganisms (such as bacteria or viruses), or antigenic proteins, peptides or DNA derived from them. In some cases, the vaccine is a subunit vaccine, which is an immunizing agent that has been treated to remove traces of nucleic acid (such as viral nucleic acid) so that only protein subunits remain. The subunits have less risk of causing adverse reactions. The vaccine can also be a live vaccine, which is a vaccine prepared from living attenuated organisms or from viruses that have been attenuated but can still replicate in the cells of the host organism.

The immunogenic material for a cancer vaccine may include, for example, a protein or peptide expressed by a tumor or cancer cell. Vaccines may elicit both prophylactic (preventative) and therapeutic responses. Methods of administration vary according to the vaccine, but may include inoculation, ingestion, inhalation or other forms of administration.

Unless otherwise explained, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Hence “comprising A or B” means including A, or B, or A and B. It is further to be understood that all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for description. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. All publications, patent applications, patents, GENBANK™ Accession numbers and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

III. Overview of Several Embodiments

There are three phases of a virus-specific CD8⁺ T cell response after virus infection (FIG. 1). First, naïve virus-specific CD8⁺ T cells exponentially expand and become effector T cells. These effector T cells stop proliferating approximately 1 to 2 weeks after infection and enter the contraction phase. During the contraction phase, effector CD8⁺ T cells gradually acquire memory T cell phenotype and function.

Disclosed herein is the surprising finding that treatment with an mTOR inhibitor enhances T cell immune responses. To enhance antigen-specific T cell immune responses in a subject, an mTOR inhibitor is administered during the contraction phase of a T cell response, or is administered at any time prior to or subsequent to antigen challenge when administered at a low dose. Thus, provided herein is a method of enhancing an antigen-specific T cell response in a subject exposed to an antigen by administering to the subject a therapeutically effective amount of an mTOR inhibitor, thereby enhancing a T cell immune response in a subject.

The subject in need of treatment can be any subject exposed to an antigen, such as antigen from a pathogen during a viral, bacterial, fungal or parasitic infection. In some cases, the subject in need of treatment is a subject with a tumor who is exposed to a tumor antigen expressed by the tumor or cancer cells. The subject in need of treatment can also be exposed to an antigen that is a component of a vaccine, such as for prophylactic treatment of a disease (including, for example, an infectious disease or cancer).

In particular embodiments, provided herein is a method of enhancing an antigen-specific T cell response in a subject in need of treatment by administering to the subject a therapeutically effective amount of an an antigen and a therapeutically effective amount of an mTOR inhibitor, thereby enhancing a T cell immune response in a subject.

In some embodiments, the T cells are CD8⁺ T cells or CD4⁺ T cells, or both. The CD8⁺ or CD4⁺ T cells can be effector T cells or memory T cells.

In some embodiments, enhancing an antigen-specific T cell response in a subject exposed to an antigen includes increasing the number of CD8⁺ T cells, enhancing the quality of CD8⁺ T cells, or both.

In some embodiments, the CD8⁺ T cells are CD8⁺ effector T cells. In some embodiments, enhancing the quality of CD8⁺ effector T cells is characterized by an increase in the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells in a subject relative to a control, such as the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells prior to or in the absence of treatment with an mTOR inhibitor. The control can also be a historical or reference value.

In some embodiments, the CD8⁺ T cells are CD8⁺ memory T cells. In some embodiments, enhancing the quality of CD8⁺ memory T cells is characterized by an increase in expression of CD127, an increase in expression of CD62L, an increase in expression of Bcl-2, an increase in expression of CD27, a decrease in expression of KLRG, or a combination thereof. In some examples, a decrease in expression of a T cell marker is a decrease of at least about 10%, at least about 20%, at least about 30%, at least about 40%, or at least about 50%. In some examples, an increase in expression of a T cell marker is an increase of at least about 10%, at least about 20%, at least about 30%, at least about 40%, or at least about 50%. The increase or decrease in expression of the T cell marker is relative to a control, such as expression level prior to or in the absence of treatment with an mTOR inhibitor. The control can also be a historical or reference value.

In some embodiments, enhancing an antigen-specific T cell response comprises increasing the number of CD4⁺ T cells, enhancing the quality of CD4⁺ T cells, or both. In some embodiments, the CD4⁺ T cells are CD4⁺ memory T cells.

In some embodiments, the antigen administered to the subject is a component of a vaccine.

The antigen can be any type of antigen against which an immune response is desired, such as an antigen from a pathogen, or a tumor antigen or antigen that is part of a vaccine. Accordingly, a subject can be exposed to an antigen, such as occurs during an infection with a pathogen or with development of cancer, or a subject can be administered the antigen, such as by prophylactic or therapeutic immunization with a vaccine. In some embodiments, the antigen is from a pathogen, such as, but not limited to a virus, bacterium, fungus or parasite. The antigen from the pathogen is any protein or other molecule capable of eliciting an immune response in a subject exposed to the antigen. In some examples, the antigen is a virus, such as human immunodeficiency virus (HIV) or hepatitis B virus (HBV). In some embodiments, the subject has an acute infection. For example, influenza viruses and rhinoviruses typically cause acute infections. In other embodiments, the subject has a chronic infection. Examples of chronic infections include, but are not limited to, hepatitis C virus infection (HCV) and HIV infection.

In some embodiments, the antigen is a tumor antigen. In one embodiment, the tumor is a hematologic cancer. In some examples, the hematologic cancer is leukemia or lymphoma, such as lymphocytic leukemia, myelogenous leukemia, myelocytic leukemia, Hodgkin's disease, non-Hodgkin's lymphoma and multiple myeloma. In another embodiment, the tumor is a solid tumor. In some examples, the solid tumor is a carcinoma, melanoma, sarcoma or central nervous system tumor. Examples of solid tumors include, but are not limited to hepatocellular carcinoma, malignant melanoma, colon cancer, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer and retinoblastoma.

In some embodiments of the methods of enhancing a T cell response in a subject, the subject is naturally exposed to the antigen such as via an infection with a pathogen, or due to the development of a tumor. In these cases, the mTOR inhibitor is generally administered following exposure to the antigen to augment T cell immune responses in the exposed subject.

In some embodiments, the method of an enhancing a T cell response in a subject further comprises administering a vaccine to the subject. In one embodiment, the vaccine is a vaccine against a pathogen, such as a virus. In another embodiment, the vaccine is a cancer vaccine.

In some embodiments, the mTOR inhibitor is administered prior to administration of the antigen (such as by administration of a vaccine). In one embodiment, the mTOR inhibitor is administered up to three days prior to administration of the antigen. In another embodiment, the mTOR inhibitor is administered up to one day prior to administration of the antigen.

In some embodiments, the mTOR inhibitor is administered after administration of the antigen. In one embodiment, the mTOR inhibitor is administered up to 20 days following administration of the antigen. In some examples, the mTOR inhibitor is administered 7 to 20 days following administration of the antigen. In other examples, the mTOR inhibitor is administered 10 to 15 days following administration of the antigen. In some embodiments, the mTOR inhibitor is administered on the same day as the antigen, including, but not limited to, within 5 minutes, within 10 minutes, or within 15 minutes of administration of the antigen. In some examples, the mTOR inhibitor is administered simultaneously, such as within 0 to 5 minutes of administration of the vaccine. In other examples, the mTOR inhibitor is administered within 5 to 15 minutes of administration of the antigen.

In some embodiment, the mTOR inhibitor is administered in a single dose. In other embodiments, the mTOR inhibitor is administered in multiple doses. In some examples, the mTOR inhibitor is administered in 1 to 40 doses, such as 5 to 30 doses, 10 to 25 doses, or 15 to 20 doses. When administered in multiple doses, the mTOR inhibitor can be administered prior to, on the same day as, or following administration of the antigen, or a combination thereof. For example, a subject can be administered the mTOR inhibitor daily for three days prior to administration of the antigen and daily for one week following immunization. As another example, a subject can be administered the mTOR inhibitor on the same day as the antigen and then administered the mTOR inhibitor daily for up to one week. In some embodiments, the mTOR inhibitor is administered daily. In some examples, the mTOR inhibitor is administered daily for one week. In other embodiments, the mTOR inhibitor is administered weekly.

In some embodiments, the mTOR inhibitor is administered continuously, such as part of a patch or other transdermal delivery means.

In some embodiments, the mTOR inhibitor is rapamycin or a rapamycin analog. In one embodiment, the dose of rapamycin is about 0.2 to about 1.0 mg/kg, such as about 0.4 to about 0.8 mg/kg. In some examples, the dose of rapamycin is about 0.2, about 0.3, about 0.4, about 0.5, about 0.6, about 0.7, about 0.8, about 0.0 or about 1.0 mg/kg. In another embodiment, the dose of rapamycin is a low dose of rapamycin. In one embodiment, the low dose of rapamycin is about 0.01 to about 0.15 mg/kg, such as about 0.05 to about 0.1 mg/kg. In some examples, a low dose of rapamycin is about 0.01, about 0.02, about 0.03, about 0.04, about 0.05, about 0.06, about 0.07, about 0.08, about 0.09, about 0.10, about 0.11, about 0.12, about 0.13, about 0.14 or about 0.15 mg/kg. In this context, “about” refers to a value within 0.005 mg/kg.

When a low dose of rapamycin (or another mTOR inhibitor) is used, administration can occur at any time relative to exposure to or administration of the antigen. When a higher dose of inhibitor is used, it is typically effective when delivered to a subject after exposure to the antigen, such as up to about 10, up to about 15 days or up to about 20 days following exposure, which correlates with the T cell contraction phase of an immune response in humans (Miller et al., Immunity 28(5):710-722, 2008). In some examples, the higher dose of rapamycin is administered 7 to 20 days following exposure to or administration of antigen.

In some embodiments, the method further comprises measuring the number of antigen-specific T cells in a sample obtained from the subject. In other embodiments, the method further comprises measuring the expression of one or more of CD127, CD62L, Bcl-2, CD27 and KLRG-1 in T cells from a sample obtained from the subject.

Also provided herein is a method of increasing the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells in a subject, comprising administering to the subject a therapeutically effective amount of an antigen and an mTOR inhibitor, thereby increasing the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells in the subject. In some embodiments, an increase in the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells is relative to the proportion of CD127^(High)KLRG-1^(Low) CD8⁺ T cells in the absence of treatment. In some embodiments, the subject has an acute or chronic infection, or has a tumor.

In some examples, the method of increasing the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells in a subject exposed to an antigen, comprises (i) selecting a subject in need of treatment; (ii) administering to the subject an mTOR inhibitor; and (iii) measuring the proportion of antigen-specific CD127^(High)KLRG-1^(Low) CD8⁺ T cells in the subject relative to the proportion of CD127^(High)KLRG-1^(Low) CD8⁺ T cells in the absence of treatment.

Further provided is a method of increasing expression of CD127, CD62L, Bcl-2 and CD27, and decreasing expression of KLRG-1, in CD8⁺ T cells of a subject, comprising administering to the subject a therapeutically effective amount of an antigen and an mTOR inhibitor, thereby increasing expression of CD127, CD62L, Bcl-2 and CD27, and decreasing expression of KLRG-1, in CD8⁺ T cells of the subject. In some embodiments, the increase or decrease in expression of the T cell markers is relative to expression in the absence of treatment. In some embodiments, the subject has an acute or chronic infection, or has a tumor.

In some examples, the method of increasing expression of CD127, CD62L, Bcl-2 and CD27, and decreasing expression of KLRG-1, in CD8⁺ T cells of a subject exposed to an antigen comprises (i) selecting a subject in need of treatment; (ii) administering to the subject an mTOR inhibitor; and (iii) measuring expression of CD127, CD62L, Bcl-2, CD27 and KLRG-1 in CD8⁺ T cells of a subject relative to expression in the absence of treatment.

Also provided is the use of an mTOR inhibitor and a vaccine comprising an antigen in the manufacture of a medicament for enhancing an antigen-specific T cell response in a subject, wherein enhancing an antigen-specific T cell response in a subject comprises increasing the number of antigen-specific T cells or enhancing the quality of antigen-specific T cells in the subject.

Also provided herein are compositions comprising an mTOR inhibitor and an antigen and/or a vaccine. In some embodiments, the vaccine is a live vaccine. In some embodiments, the vaccine is a subunit vaccine. In some embodiments, the compositions comprise an mTOR inhibitor, purified antigen and an adjuvant. The antigen can be any antigen, such as an antigen from a pathogen, a tumor antigen or a vaccine antigen. Suitable antigens are described herein and are well known in the art. In some embodiments, the compositions provided herein further comprise a pharmaceutically acceptable carrier. Further provided is the use of such compositions in the manufacture of a medicament for enhancing an antigen-specific T cell response in a subject.

IV. Mammalian Target of Rapamycin (mTOR) Inhibitors

Inhibitors of mTOR for use with the methods claimed herein can be any type of molecule that inhibits expression or activity of mTOR. For example, mTOR inhibitors, include, but are not limited to small molecules, synthetic compounds, antibodies, peptides and nucleic acids (including, for example, antisense oligonucleotides, small interfering RNA (siRNA), short hairpin RNA, microRNA, ribozymes and the like).

A. Small Molecule Inhibitors

A number of small molecule mTOR inhibitors are known, some of which are currently being used to treat a variety of diseases. In addition, a number of mTOR inhibitors are under investigation in clinical trials for treating of diseases such as cancer. The best characterized mTOR inhibitor is rapamycin, a naturally occurring small molecule with known immunosuppressive and anti-proliferative properties. Rapamycin, also known as sirolimus, is a macrolide that was first discovered as a product of the bacterium Streptomyces hygroscopicus. Rapamycin binds and inhibits the activity of mTOR. Rapamycin is also marketed under the name RAPAMUNE™. Provided in Table 1 below is a list of some of the mTOR inhibitors currently being tested in clinical trials.

TABLE 1 mTOR inhibitors under evaluation in clinical trials Compound Company Description RAD001 Novartis Orally available derivative of rapamycin OSI-027 OSI Pharmaceuticals Inhibits the kinase activity associated with both the mTORC1 and mTORC2 complexes AP23573 Ariad Pharmaceuticals Rapamycin analog AP23675 Ariad Pharmaceuticals Rapamycin analog AP23841 Ariad Pharmaceuticals Rapamycin analog ABI-009 Abraxis Bioscience Inc. mTOR inhibitor MK8669 Merck & Co. mTOR inhibitor TOP216 Topotarget A/S mTOR inhibitor TAFA93 Isotechnika Inc. Prodrug of rapamycin TORISEL ™ Wyeth Pharmaceuticals mTOR inhibitor CERTICAN ™ Novartis AG mTOR inhibitor

Additional mTOR inhibitors, including rapamycin derivatives and analogs have been described, such as, for example, those disclosed in PCT Publication Nos. WO 2007/135411, WO 98/02441, WO 01/14387 and WO 03/64383; and European Patent No. EP1880723.

B. Antisense Compounds

In addition to small molecule inhibitors, antisense compounds that specifically target and down-regulate expression of mTOR can be used with the methods provided herein. Generally, the principle behind antisense technology is that an antisense compound hybridizes to a target nucleic acid and effects the modulation of gene expression activity, or function, such as transcription, translation or splicing. The modulation of gene expression can be achieved by, for example, target RNA degradation or occupancy-based inhibition. An example of modulation of target RNA function by degradation is RNase H-based degradation of the target RNA upon hybridization with a DNA-like antisense compound, such as an antisense oligonucleotide. Antisense oligonucleotides can also be used to modulate gene expression, such as splicing, by occupancy-based inhibition, such as by blocking access to splice sites.

Another example of modulation of gene expression by target degradation is RNA interference (RNAi) using small interfering RNAs (siRNAs). RNAi is a form of antisense-mediated gene silencing involving the introduction of double stranded RNA-like oligonucleotides leading to the sequence-specific reduction of targeted endogenous mRNA levels. Another type of antisense compound that utilizes the RNAi pathway is a microRNA. MicroRNAs are naturally occurring RNAs involved in the regulation of gene expression. However, these compounds can be synthesized to regulate gene expression via the RNAi pathway. Similarly, short hairpin RNAs (shRNAs) are RNA molecules that form a tight hairpin turn and can be used to silence gene expression via the RNAi pathway. The shRNA hairpin structure is cleaved by the cellular machinery into siRNA.

Other compounds that are often classified as antisense compounds are ribozymes. Ribozymes are catalytic RNA molecules that can bind to specific sites on other RNA molecules and catalyze the hydrolysis of phosphodiester bonds in the RNA molecules. Ribozymes modulate gene expression by direct cleavage of a target nucleic acid, such as a messenger RNA.

Each of the above-described antisense compounds provides sequence-specific target gene regulation. This sequence-specificity makes antisense compounds effective tools for the selective modulation of a target nucleic acid of interest, such as mTOR.

Any type of antisense compound that specifically targets and regulates expression of mTOR is contemplated for use with the disclosed methods. Such antisense compounds include single-stranded compounds, such as antisense oligonucleotides, and double-stranded compounds, including compounds with at least partial double-stranded structure, including siRNAs, miRNAs, shRNAs and ribozymes. Methods of designing, preparing and using antisense compounds that specifically target mTOR are within the abilities of one of skill in the art.

Furthermore, sequences for mTOR are publicly available. Exemplary human mTOR nucleotide sequences are provided herein as SEQ ID NO: 3 (GENBANK™ Accession No. NM_004958, deposited on Apr. 4, 2002) and SEQ ID NO: 5 (GENBANK™ Accession No. BC117166, deposited on Jun. 26, 2006). Antisense compounds specifically targeting mTOR can be prepared by designing compounds that are complementary to an mTOR nucleotide sequence, particularly the mTOR mRNA sequence. Antisense compounds targeting mTOR need not be 100% complementary to mTOR to specifically hybridize and regulate expression the target gene. For example, the antisense compound, or antisense strand of the compound if a double-stranded compound, can be at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or 100% complementary to the selected mTOR nucleic acid sequence. Methods of screening antisense compounds for specificity are well known in the art (see, for example, U.S. Patent Application Publication No. 2003-0228689). Exemplary mTOR shRNA sequences are provided herein as SEQ ID NOs: 10 and 11.

C. Antibodies Specific for mTOR

An mTOR polypeptide or a fragment or conservative variant thereof can be used to produce antibodies which are immunoreactive or specifically bind to an epitope of an mTOR. Polyclonal antibodies, antibodies which consist essentially of pooled monoclonal antibodies with different epitopic specificities, as well as distinct monoclonal antibody preparations are included.

The preparation of polyclonal antibodies is well known to those skilled in the art. See, for example, Green et al., “Production of Polyclonal Antisera,” in: Immunochemical Protocols, pages 1-5, Manson, ed., Humana Press, 1992; Coligan et al., “Production of Polyclonal Antisera in Rabbits, Rats, Mice and Hamsters,” in: Current Protocols in Immunology, section 2.4.1, 1992.

The preparation of monoclonal antibodies likewise is conventional (see, for example, Kohler & Milstein, Nature 256:495, 1975; Coligan et al., sections 2.5.1-2.6.7; and Harlow et al. in: Antibodies: a Laboratory Manual, page 726, Cold Spring Harbor Pub., 1988). Briefly, monoclonal antibodies can be obtained by injecting mice with a composition comprising an antigen, verifying the presence of antibody production by removing a serum sample, removing the spleen to obtain B lymphocytes, fusing the B lymphocytes with myeloma cells to produce hybridomas, cloning the hybridomas, selecting positive clones that produce antibodies to the antigen, and isolating the antibodies from the hybridoma cultures. Monoclonal antibodies can be isolated and purified from hybridoma cultures by a variety of well-established techniques. Such isolation techniques include affinity chromatography with Protein-A Sepharose, size-exclusion chromatography, and ion-exchange chromatography (see, e.g., Coligan et al., sections 2.7.1-2.7.12 and sections 2.9.1-2.9.3; Barnes et al., Purification of Immunoglobulin G (IgG), in: Methods in Molecular Biology, Vol. 10, pages 79-104, Humana Press, 1992).

Methods of in vitro and in vivo multiplication of monoclonal antibodies are well known to those skilled in the art. Multiplication in vitro may be carried out in suitable culture media such as Dulbecco's Modified Eagle Medium or RPMI 1640 medium, optionally supplemented by a mammalian serum such as fetal calf serum or trace elements and growth-sustaining supplements such as normal mouse peritoneal exudate cells, spleen cells, thymocytes or bone marrow macrophages. Production in vitro provides relatively pure antibody preparations and allows scale-up to yield large amounts of the desired antibodies. Large-scale hybridoma cultivation can be carried out by homogenous suspension culture in an airlift reactor, in a continuous stirrer reactor, or in immobilized or entrapped cell culture. Multiplication in vivo may be carried out by injecting cell clones into mammals histocompatible with the parent cells, such as syngeneic mice, to cause growth of antibody-producing tumors. Optionally, the animals are primed with a hydrocarbon, especially oils such as pristane (tetramethylpentadecane) prior to injection. After one to three weeks, the desired monoclonal antibody is recovered from the body fluid of the animal.

Antibodies can also be derived from a subhuman primate antibody. General techniques for raising therapeutically useful antibodies in baboons can be found, for example, in PCT Publication No. WO 91/11465, 1991; and Losman et al., Int. J. Cancer 46:310, 1990.

Alternatively, an antibody that specifically binds an mTOR polypeptide can be derived from a humanized monoclonal antibody. Humanized monoclonal antibodies are produced by transferring complementarity determining regions from another species such as a mouse from heavy and light variable chains of the immunoglobulin into a human variable domain, and then substituting human residues in the framework regions of the murine counterparts. The use of antibody components derived from humanized monoclonal antibodies obviates potential problems associated with the immunogenicity of murine constant regions. General techniques for cloning murine immunoglobulin variable domains are described, for example, by Orlandi et al., Proc. Natl. Acad. Sci. U.S.A. 86:3833, 1989. Techniques for producing humanized monoclonal antibodies are described, for example, by Jones et al., Nature 321:522, 1986; Riechmann et al., Nature 332:323, 1988; Verhoeyen et al., Science 239:1534, 1988; Carter et al., Proc. Natl. Acad. Sci. U.S.A. 89:4285, 1992; Sandhu, Crit. Rev. Biotech. 12:437, 1992; and Singer et al., J. Immunol. 150:2844, 1993.

Antibodies can be derived from human antibody fragments isolated from a combinatorial immunoglobulin library. See, for example, Barbas et al., in: Methods: a Companion to Methods in Enzymology, Vol. 2, page 119, 1991; Winter et al., Ann. Rev. Immunol. 12:433, 1994. Cloning and expression vectors that are useful for producing a human immunoglobulin phage library can be obtained, for example, from STRATAGENE Cloning Systems (La Jolla, Calif.).

In addition, antibodies can be derived from a human monoclonal antibody. Such antibodies can be obtained from transgenic mice that have been “engineered” to produce specific human antibodies in response to antigenic challenge. In this technique, elements of the human heavy and light chain loci are introduced into strains of mice derived from embryonic stem cell lines that contain targeted disruptions of the endogenous heavy and light chain loci. The transgenic mice can synthesize human antibodies specific for human antigens, and the mice can be used to produce human antibody-secreting hybridomas. Methods for obtaining human antibodies from transgenic mice are described by Green et al., Nature Genet. 7:13, 1994; Lonberg et al., Nature 368:856, 1994; and Taylor et al., Int. Immunol. 6:579, 1994.

Antibodies include intact molecules as well as fragments thereof, such as Fab, F(ab′)2, and Fv which are capable of binding the epitopic determinant. These antibody fragments retain some ability to selectively bind with their antigen or receptor and are defined as follows:

(1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;

(2) Fab′, the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule;

(3) (Fab′)₂, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′)2 is a dimer of two Fab′ fragments held together by two disulfide bonds;

(4) Fv, defined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and

(5) Single chain antibody (SCA), defined as a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule.

Methods of making these fragments are known in the art (see for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 1988). An epitope is any antigenic determinant on an antigen to which the paratope of an antibody binds. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics.

Antibody fragments can be prepared by proteolytic hydrolysis of the antibody or by expression in E. coli of DNA encoding the fragment. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab′)2. This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab′ monovalent fragments. Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab′ fragments and an Fc fragment directly (see U.S. Pat. No. 4,036,945 and U.S. Pat. No. 4,331,647, and references contained therein; Nisonhoff et al., Arch. Biochem. Biophys. 89:230, 1960; Porter, Biochem. J. 73:119, 1959; Edelman et al., Methods in Enzymology, Vol. 1, page 422, Academic Press, 1967; and Coligan et al. at sections 2.8.1-2.8.10 and 2.10.1-2.10.4).

Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical, or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody.

For example, Fv fragments comprise an association of V_(H) and V_(L) chains. This association may be noncovalent (Inbar et al., Proc. Natl. Acad. Sci. U.S.A. 69:2659, 1972). Alternatively, the variable chains can be linked by an intermolecular disulfide bond or cross-linked by chemicals such as glutaraldehyde (see, for example, Sandhu, Crit. Rev. Biotech. 12:437, 1992). Preferably, the Fv fragments comprise V_(H) and V_(L) chains connected by a peptide linker. These single-chain antigen binding proteins (sFv) are prepared by constructing a structural gene comprising DNA sequences encoding the V_(H) and V_(L) domains connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing sFvs are known in the art (see Whitlow et al., Methods: a Companion to Methods in Enzymology, Vol. 2, page 97, 1991; Bird et al., Science 242:423, 1988; U.S. Pat. No. 4,946,778; Pack et al., Bio/Technology 11:1271, 1993; and Sandhu, supra).

Antibodies can be prepared using an intact polypeptide or fragments containing small peptides of interest as the immunizing antigen. The polypeptide or a peptide used to immunize an animal can be derived from substantially purified polypeptide produced in host cells, in vitro translated cDNA, or chemical synthesis which can be conjugated to a carrier protein, if desired. Such commonly used carriers which are chemically coupled to the peptide include keyhole limpet hemocyanin, thyroglobulin, bovine serum albumin, and tetanus toxoid. The coupled peptide is then used to immunize the animal (e.g., a mouse, a rat, or a rabbit).

Polyclonal or monoclonal antibodies can be further purified, for example, by binding to and elution from a matrix to which the polypeptide or a peptide to which the antibodies were raised is bound. Those of skill in the art will know of various techniques common in the immunology arts for purification and/or concentration of polyclonal antibodies, as well as monoclonal antibodies (see, for example, Coligan et al., Unit 9, Current Protocols in Immunology, Wiley Interscience, 1991).

V. Antigens and Vaccines

As described herein, administration of an mTOR inhibitor in conjunction with exposure to an antigen or administration of a vaccine, enhances antigen-specific T cell immune responses. The antigen can be any type of antigen against which an immune response is desired in a subject, or any antigen to which a subject is exposed. In some cases, a subject is exposed to the antigen during an infection, such as a viral, bacterial, fungal or parasitic infection. In other cases, the subject has a tumor and is exposed to a tumor-specific antigen. Alternatively, the antigen can be administered to a subject, such as in the form of a vaccine. In some embodiments, the vaccine is a vaccine against a pathogen, or a cancer vaccine.

A. Antigens

In some embodiments, the antigen is an antigen from a pathogen, such as a virus, bacterium, fungus or parasite. Viral pathogens include, but are not limited to retroviruses, such as human immunodeficiency virus (HIV) and human T-cell leukemia viruses; picornaviruses, such as polio virus, hepatitis A virus; hepatitis C virus, enteroviruses, human coxsackie viruses, rhinoviruses, echoviruses, and foot-and-mouth disease virus; caliciviruses, such as strains that cause gastroenteritis (e.g., Norwalk virus); togaviruses, such as alphaviruses (including chikungunya virus, equine encephalitis viruses, Sindbis virus, Semliki Forest virus, and Ross River virus) and rubella virus; flaviviruses, such as dengue viruses, yellow fever viruses, West Nile virus, St. Louis encephalitis virus, Japanese encephalitis virus, Powassan virus and other encephalitis viruses; coronaviruses, including severe acute respiratory syndrome (SARS) virus; rhabdoviruses, such as vesicular stomatitis virus and rabies virus; filoviruses, such as Ebola virus and Marburg virus); paramyxoviruses, such as parainfluenza virus, mumps virus, measles virus, and respiratory syncytial virus; orthomyxoviruses, such as influenza viruses (including avian influenza viruses and swine influenza viruses); bunyaviruses, such as Hantaan virus; Sin Nombre virus, and Rift Valley fever virus, phleboviruses and Nairo viruses; arenaviruses, such as Lassa fever virus and other hemorrhagic fever viruses, Machupo virus and Junin virus; reoviruses, such as mammalian reoviruses, orbiviurses and rotaviruses; birnaviruses; hepadnaviruses, such as hepatitis B virus; parvoviruses; papovaviruses, such as papilloma viruses, polyoma viruses and BK-virus; adenoviruses; herpesviruses, such as herpes simplex virus (HSV)-1 and HSV-2, cytomegalovirus, Epstein-Barr virus, varicella zoster virus, and other herpes viruses, including HSV-6); pox viruses, such as variola viruses and vaccinia viruses; irodoviruses, such as African swine fever virus; astroviruses; and unclassified viruses (for example, the etiological agents of spongiform encephalopathies, the agent of delta hepatitis (thought to be a defective satellite of hepatitis B virus).

Bacterial pathogens include, but are not limited to Helicobacter pylori, Escherichia coli, Vibrio cholerae, Borelia burgdorferi, Legionella pneumophilia, Mycobacteria sps (such as. M. tuberculosis, M. avium, M. intracellulare, M. kansai and, M. gordonae), Staphylococcus aureus, Neisseria gonorrhoeae, Neisseria meningitidis, Listeria monocytogenes, Streptococcus pyogenes (Group A Streptococcus), Streptococcus agalactiae (Group B Streptococcus), Streptococcus (viridans group), Streptococcus faecalis, Streptococcus bovis, Streptococcus (anaerobic sps.), Streptococcus pneumoniae, pathogenic Campylobacter sp., Enterococcus sp., Haemophilus influenzae, Bacillus anthracis, Corynebacterium diphtheriae, corynebacterium sp., Erysipelothrix rhusiopathiae, Clostridium perfringers, Clostridium tetani, Enterobacter aerogenes, Klebsiella pneumoniae, Pasteurella multocida, Bacteroides sp., Fusobacterium nucleatum, Streptobacillus moniliformis, Treponema pallidium, Treponema pertenue, Leptospira, Bordetella pertussis, Shigella flexnerii, Shigella dysenteriae and Actinomyces israelli.

Fungal pathogens include, but are not limited to Cryptococcus neoformans, Histoplasma capsulatum, Coccidioides immitis, Blastomyces dermatitidis, Chlamydia trachomatis, Candida albicans. Parasitic pathogens include, but are not limited to Plasmodium falciparum, Plasmodium vivax, Trypanosoma cruzi and Toxoplasma gondii.

In some cases, the antigen is a tumor-associated antigen. Tumor antigens are proteins that are produced by tumor cells that elicit an immune response, particularly T-cell mediated immune responses. The tumor antigen can be any tumor-associated antigen, which are well known in the art and include, for example, carcinoembryonic antigen (CEA), β-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut hsp70-2, macrophage colony stimulating factor, prostase, prostate-specific antigen (PSA), PAP, NY-ESO-1, LAGE-1a, p53, prostein, PSMA, Her2/neu, survivin and telomerase, prostate-carcinoma tumor antigen-1, MAGE, ELF2M, neutrophil elastase, ephrinB2, CD22, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor and mesothelin. A list of selected tumor antigens and their associated tumors are shown below in Table 2.

TABLE 2 Exemplary tumors and their tumor antigens Tumor Tumor Associated Target Antigens Acute myelogenous leukemia Wilms tumor 1 (WT1), PRAME, PR1, proteinase 3, elastase, cathepsin G Chronic myelogenous leukemia WT1, PRAME, PR1, proteinase 3, elastase, cathepsin G Myelodysplastic syndrome WT1, PRAME, PR1, proteinase 3, elastase, cathepsin G Acute lymphoblastic leukemia PRAME Chronic lymphocytic leukemia Survivin Non-Hodgkin's lymphoma Survivin Multiple myeloma NY-ESO-1 Malignant melanoma MAGE, MART, Tyrosinase, PRAME GP100 Breast cancer WT1, herceptin, epithelial tumor antigen (ETA) Lung cancer WT1 Ovarian cancer CA-125 Prostate cancer PSA Pancreatic cancer CA19-9, RCAS1 Colon cancer CEA Renal cell carcinoma (RCC) Fibroblast growth factor 5 Germ cell tumors AFP

In some embodiments, a subject is administered an mTOR inhibitor following diagnosis of the subject (e.g. a diagnosis of the presence of an infection or cancer). The mTOR inhibitor can be administered in a single dose or in multiple doses over time. In some examples, a subject having an infection or cancer is administered an mTOR inhibitor daily for at least one week, at least one month or at least three months.

B. Vaccines

In some embodiments, the antigen is delivered as part of a vaccine. A number of vaccines against infectious diseases are currently approved for use in the United States, examples of which are listed below in Table 3.

TABLE 3 Approved Vaccines for Immunization and Distribution in the U.S. Product Name Trade Name Anthrax Vaccine Adsorbed BIOTHRAX BCG Vaccine TICE BCG BCG Vaccine MYCOBAX Diphtheria & Tetanus Toxoids Adsorbed None Diphtheria & Tetanus Toxoids Adsorbed None Diphtheria & Tetanus Toxoids & Acellular Pertussis TRIPEDIA Vaccine Adsorbed Diphtheria & Tetanus Toxoids & Acellular Pertussis INFANRIX Vaccine Adsorbed Diphtheria & Tetanus Toxoids & Acellular Pertussis DAPTACEL Vaccine Adsorbed Diphtheria & Tetanus Toxoids & Acellular Pertussis PEDIARIX Vaccine Adsorbed, Hepatitis B (recombinant) and Inactivated Poliovirus Vaccine Combined Diphtheria and Tetanus Toxoids and Acellular KINRIX Pertussis Adsorbed and Inactivated Poliovirus Vaccine Diphtheria and Tetanus Toxoids and Acellular PENTACEL Pertussis Adsorbed, Inactivated Poliovirus and Haemophilus b Conjugate (Tetanus Toxoid Conjugate) Vaccine Haemophilus b Conjugate Vaccine (Diphtheria HIBTITER CRM197 Protein Conjugate) Haemophilus b Conjugate Vaccine (Meningococcal PEDVAXHIB Protein Conjugate) Haemophilus b Conjugate Vaccine (Tetanus Toxoid ACTHIB Conjugate) Haemophilus b Conjugate Vaccine (Meningococcal COMVAX Protein Conjugate) & Hepatitis B Vaccine (Recombinant) Hepatitis A Vaccine, Inactivated HAVRIX Hepatitis A Vaccine, Inactivated VAQTA Hepatitis A Inactivated and Hepatitis B TWINRIX (Recombinant) Vaccine Hepatitis B Vaccine (Recombinant) RECOMBIVAX HB Hepatitis B Vaccine (Recombinant) ENGERIX-B Human Papillomavirus (Types 6, 11, 16, 18) GARDASIL Recombinant Vaccine Influenza Virus Vaccine AFLURIA Influenza Virus Vaccine, H5N1 None Influenza Virus Vaccine, Trivalent, Types A and B FLULAVAL Influenza Virus Vaccine, Live, Intranasal FLUMIST Influenza Virus Vaccine, Trivalent, Types A and B FLUARIX Influenza Virus Vaccine, Trivalent, Types A and B FLUVIRIN Influenza Virus Vaccine, Trivalent, Types A and B FLUZONE Japanese Encephalitis Virus Vaccine Inactivated JE-VAX Measles Virus Vaccine, Live ATTENUVAX Measles and Mumps Virus Vaccine, Live M-M-Vax Measles, Mumps, and Rubella Virus Vaccine, Live M-M-R II Measles, Mumps, Rubella and Varicella Virus PROQUAD Vaccine, Live Meningococcal Polysaccharide (Serogroups A, C, Y MENACTRA and W-135) Diphtheria Toxoid Conjugate Vaccine Meningococcal Polysaccharide Vaccine, Groups A, MENOMUNE- C, Y and W-135 Combined A/C/Y/W-135 Mumps Virus Vaccine Live MUMPSVAX Plague Vaccine None Pneumococcal Vaccine, Polyvalent PNEUMOVAX 23 Pneumococcal 7-valent Conjugate Vaccine PREVNAR (Diphtheria CRM197 Protein) Poliovirus Vaccine Inactivated (Human Diploid POLIOVAX Cell) Poliovirus Vaccine Inactivated (Monkey Kidney IPOL Cell) Rabies Vaccine IMOVAX Rabies Vaccine RABAVERT Rabies Vaccine Adsorbed No Trade Name Rotavirus Vaccine, Live, Oral ROTARIX Rotavirus Vaccine, Live, Oral, Pentavalent ROTATEQ Rubella Virus Vaccine Live MERUVAX II Smallpox (Vaccinia) Vaccine, Live ACAM2000 Smallpox Vaccine, Dried, Calf Lymph Type DRYVAX Tetanus & Diphtheria Toxoids Adsorbed for Adult None Use Tetanus & Diphtheria Toxoids Adsorbed for Adult DECAVAC Use Tetanus & Diphtheria Toxoids Adsorbed for Adult TENIVAC Use Tetanus Toxoid None Tetanus Toxoid Adsorbed None Tetanus Toxoid Adsorbed None Tetanus Toxoid, Reduced Diphtheria Toxoid and ADACEL Acellular Pertussis Vaccine, Adsorbed Tetanus Toxoid, Reduced Diphtheria Toxoid and BOOSTRIX Acellular Pertussis Vaccine, Adsorbed Typhoid Vaccine Live Oral Ty21a VIVOTIF Typhoid Vi Polysaccharide Vaccine TYPHIM VI Varicella Virus Vaccine Live VARIVAX Yellow Fever Vaccine YF-VAX Zoster Vaccine, Live ZOSTAVAX

With the exception of the HPV and HBV vaccines that prevent cervical cancer and liver cancer, respectively, as a result of inhibiting virus infection, there are currently no cancer vaccines approved for clinical use. However, a number of vaccine candidates are being evaluated for a wide variety of different types of cancer. For example, candidate tumor vaccines include, but are not limited to, antigen/adjuvant vaccines (cancer-specific antigenic protein fragments in combination with an adjuvant); whole-cell tumor vaccines (tumor cells taken from a subject's own tumor or the tumor of another patient); dendritic cell (DC) vaccines (DCs are isolated from a patient, stimulated ex vivo with the patient's cancer antigens and re-injected in the patient); DNA vaccines (nucleic acids encoding the sequence of a tumor antigen); and idiotype vaccines (antibodies specifically produced by a cancer cell). Accordingly, mTOR inhibitors can be used in conjunction with any such vaccine developed for eliciting immune responses against cancer.

A subject to be vaccinated can be administered an mTOR inhibitor prior to vaccination, at the same time as vaccination, following vaccination, or a combination thereof. An mTOR inhibitor can be administered in a single dose or multiple doses. Administration of mTOR inhibitors is discussed in detail below.

VI. Administration of mTOR Inhibitors

Administration of an mTOR inhibitor in accordance with the methods described herein can occur prior to, at the same time as, or following exposure to or delivery of an antigen or vaccine. The timing of administration depends in part on the dose of mTOR inhibitor administered. Low doses of mTOR inhibitor, such as rapamycin or a rapamycin analog, can be administered at any time relative to exposure of an antigen. Higher doses of mTOR inhibitor are more effective when delivered following exposure to an antigen or delivery of a vaccine, such as up to about 10 days, up to about 15 days, or up to about 20 days following exposure/delivery, which correlates with the T cell contraction phase of an immune response (Miller et al., Immunity 28(5):710-722, 2008).

In some embodiments, the mTOR inhibitor is administered up to three days prior to administration of a vaccine or exposure to an antigen. In some embodiments, the mTOR inhibitor is administered up to one day prior to administration of a vaccine or exposure to an antigen.

In some embodiments, the mTOR inhibitor is administered on the same day as the vaccine. As used herein, “on the same day” refers to administration that occurs within 24 hours (either before or after) administration of the vaccine. In some examples, the mTOR inhibitor is administered at the same time as the vaccine, such as within 0 to 5 minutes, within 5 to 10 minutes or within 10 to 15 minutes of administration of the vaccine. In some examples, the mTOR inhibitor is administered within about 15 minutes to 1 hour of administration of the vaccine. In other examples, the mTOR inhibitor is administered within about 30 minutes to about 2 hours of administration of the vaccine.

In some embodiments, the mTOR inhibitor is administered following vaccination or exposure to an antigen. In some embodiments, the mTOR inhibitor is administered up to 10 days, up to 15 days or up to 20 days after vaccination or exposure to an antigen. In some examples, the mTOR inhibitor is administered 7 to 20 days, or 10 to 15 days, following vaccination or exposure to antigen.

As described above, administration of an mTOR inhibitor can be accomplished by single or multiple doses. The dose administered to a subject should be sufficient to induce a beneficial therapeutic response (i.e. to establish sufficient immunological memory) in a subject over time, such as preventing or inhibiting infection by a pathogen, or inhibiting development or spread of a tumor. A therapeutically effective dose can also be determined by measuring the immune response, such as by detecting the number and quality of antigen-specific T cells, such as CD8⁺ or CD4⁺ memory T cells. As used herein, “multiple doses” means two or more doses, such as 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 or more doses. In some examples, the mTOR inhibitor is administered in 1 to 40 doses, such as about 5 to 30 doses, about 10 to 25 doses or about 15 to 20 doses.

The dose required will vary from subject to subject depending on the species, age, weight and general condition of the subject, the severity of the disease or disorder being treated, the particular composition being used and its mode of administration. In some embodiments, the mTOR inhibitor is rapamycin and the dose is about 0.01 to about 0.15 mg/kg, such as about 0.05 to about 0.1 mg/kg when rapamycin is administered prior to or concomitant with the antigen or vaccine. In some examples, the dose of rapamycin is about 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14 or 0.15 mg/kg. In this context, “about” refers to a value within 0.005 mg/kg. A dose of about 0.01 to about 0.15 mg/kg typically results in a blood concentration of approximately 5 to 20 ng/ml. When the mTOR inhibitor is administered prior to or concomitant with the antigen at this relatively low dose, the inhibitor can also be administered for any period of time after administration of the antigen or vaccine. In other embodiments, the mTOR inhibitor is rapamycin and the dose is about 0.2 to about 1.0 mg/kg, such as about 0.4 to about 0.8 mg/kg, when rapamycin is administered after administration of the antigen or vaccine, such as during the T cell contraction phase of an immune response. In some examples, the dose of rapamycin is about 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 or 1.0 mg/kg. In this context, “about” refers to a value within 0.05 mg/kg. A dose of about 0.2 to about 1.0 mg/kg typically results in a blood concentration of approximately 40 to 100 ng/ml. An appropriate dose can be determined by one of ordinary skill in the art using only routine experimentation.

When administered in multiple doses, the dosing schedule of the mTOR inhibitor can vary. In some embodiments, the mTOR inhibitor is administered twice a day, daily, weekly or monthly. In some embodiments, the mTOR inhibitor is administered daily for about one week. In other embodiments, the mTOR inhibitor is administered daily for about one month.

In some embodiments, the mTOR inhibitor is administered continuously, such as part of a patch or other transdermal application.

The mTOR inhibitors can be administered by any suitable route. The route of administration will be determined by a variety of factors, including the type of inhibitor used, the composition of inhibitor (e.g., liquid or solid form), and the immune response desired. Methods of administration include, but are not limited to, intradermal, topical, intramuscular, transdermal, intraperitoneal, parenteral, intravenous, subcutaneous, vaginal, rectal, intranasal, inhalation, oral or mist-spray delivery to the lungs. Parenteral administration, such as subcutaneous, intravenous or intramuscular administration, is generally achieved by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. Injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described. Administration can be systemic or local. Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with any other ingredients as required, followed by filtered sterilization.

In some embodiments, the mTOR inhibitor is administered topically or transdermally, for example in a patch, pad, bandage, cream, gel, lotion, spray, foam or paste. When administered as a patch, pad, bandage or the like, the patch, pad or bandage can be replaced at regular intervals to maintain a constant dose of mTOR inhibitor. Alternatively, the patch, pad or bandage can be applied for a given time period, such as one day, two days, three days, four days, five days, six days or seven days, or until the mTOR inhibitor is depleted from the patch, pad or bandage. Patches suitable for transdermal delivery of therapeutic agents are known in the art (see, for example, U.S. Patent Application Publication Nos. 2005/0142176; 2008/0274166; 2009/0028929; and 2009/0048567).

The mTOR inhibitors are administered in any suitable manner, such as with pharmaceutically acceptable carriers. Pharmaceutically acceptable carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions of the present disclosure.

Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like. Pharmaceutically acceptable carriers include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. The carrier and composition can be sterile, and the formulation suits the mode of administration. The composition can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. The composition can be a liquid solution, suspension, emulsion, tablet, pill, capsule, sustained release formulation, or powder. The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulations can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, and magnesium carbonate. Any of the common pharmaceutical carriers, such as sterile saline solution or sesame oil, can be used. The medium can also contain conventional pharmaceutical adjunct materials such as, for example, pharmaceutically acceptable salts to adjust the osmotic pressure, buffers, preservatives and the like. Other media that can be used with the compositions and methods provided herein are normal saline and sesame oil.

The mTOR inhibitors can be formulated in a neutral or salt form. Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or organic acids such as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.

Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required components. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. The compositions of the present invention may also be administered into the epidermis using the Powderject System (Chiron, Emeryville, Calif.). The Powderject delivery technique works by the acceleration of fine particles to supersonic speed within a helium gas jet and delivers pharmaceutical agents and vaccines to skin and mucosal injection sites, without the pain or the use of needles.

In some embodiments, the mTOR inhibitors are administered in combination with other therapeutic agents. For example, the mTOR inhibitors (or vaccine administered in conjunction with the mTOR inhibitor) can be administered with an adjuvant, such as Freund incomplete adjuvant or Freund's complete adjuvant.

Optionally, one or more cytokines, such as IL-2, IL-6, IL-12, RANTES, GM-CSF, TNF-α, or IFN-γ, one or more growth factors, such as GM-CSF or G-CSF; one or more molecules such as OX-40L or 41 BBL, or combinations of these molecules, can be used as biological adjuvants (see, for example, Salgaller et al., 1998, J. Surg. Oncol. 68(2):122-38; Lotze et al., 2000, Cancer J. Sci. Am. 6(Suppl 1):S61-6; Cao et al., 1998, Stem Cells 16(Suppl 1):251-60; Kuiper et al., 2000, Adv. Exp. Med. Biol. 465:381-90). These molecules can be administered systemically (or locally) to the host.

A number of means for inducing cellular responses, both in vitro and in vivo, are known. Lipids have been identified as agents capable of assisting in priming CTL in vivo against various antigens. For example, as described in U.S. Pat. No. 5,662,907, palmitic acid residues can be attached to the alpha and epsilon amino groups of a lysine residue and then linked (for example, via one or more linking residues, such as glycine, glycine-glycine, serine, serine-serine, or the like) to an immunogenic peptide. The lipidated peptide can then be injected directly in a micellar form, incorporated in a liposome, or emulsified in an adjuvant. As another example, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine can be used to prime tumor specific CTL when covalently attached to an appropriate peptide (see, Deres et al., Nature 342:561, 1989). Further, as the induction of neutralizing antibodies can also be primed with the same molecule conjugated to a peptide which displays an appropriate epitope, two compositions can be combined to elicit both humoral and cell-mediated responses where that is deemed desirable.

The following examples are provided to illustrate certain particular features and/or embodiments. These examples should not be construed to limit the disclosure to the particular features or embodiments described.

EXAMPLES Example 1 Rapamycin Treatment During the Contraction Phase of a CD8⁺ T Cell Response Induces High Quality Memory T Cells

This example describes the finding that rapamycin treatment (i) induces high quality memory T cells during the contraction phase of a T cell response; (ii) enhances differentiation of memory T cells during the T cell contraction phase; and (iii) enhances high quality memory T cells during the contraction phase of recall T cell responses. This example further demonstrates that memory CD8⁺ T cells induced in rapamycin treated animals are high quality memory T cells.

There are three phases of a virus-specific CD8⁺ T cell response after virus infection (FIG. 1). First, naïve virus-specific CD8⁺ T cells exponentially expand and become effector T cells. These effector T cells stop proliferating approximately 1 to 2 weeks after infection and enter the contraction phase. During the contraction phase, effector CD8⁺ T cells gradually acquire memory T cell phenotype and function.

Rapamycin is a macrolide with immunosuppressive and anti-proliferative properties. The effect of rapamycin treatment on T cell responses induced by vaccination was evaluated in mice infected with lymphocytic choriomeningitis virus (LCMV). To test the effect of rapamycin treatment on the expansion phase of a T cell response, mice were injected intraperitoneally with 2×10⁵ plaque forming units (PFU) of LCMV on Day 0 and treated with rapamycin once a day for 9 days, starting one day prior to vaccination (Day −1). Rapamycin was administered intraperitoneally at a dose of 0.6 mg/kg (resulting in blood concentration of approximately 40-100 ng/ml). On Day 8, peripheral blood mononuclear cells (PBMCs) were isolated and evaluated by FACS analysis to determine the percentage of virus-specific CD8⁺ T cells in rapamycin-treated and untreated mice (FIG. 2A). PBMCs were incubated with antibodies specific for CD8 and CD44 (a memory T cell marker), and a LCMV GP33 epitope-specific MHC class I tetramer (DbGP33; Murali-Krishna et al., Immunity 8(2):177-87, 1998). The anti-CD8 antibody was conjugated with the fluorochrome peridinin chlorophyll protein (PerCP) (BD Biosciences) and the anti-CD44 antibody was conjugated with the fluorophore Pacific Blue® (eBioscience, San Diego, Calif.). As shown in FIG. 2B, mice treated with rapamycin during the T cell expansion phase had a smaller percentage of virus-specific CD8⁺ T cells (2.49%) relative to untreated mice (6.98%), suggesting that rapamycin inhibited antigen-driven T cell proliferation. In addition, LCMV titer in rapamycin-treated mice was significantly increased relative to untreated mice (FIG. 2C), demonstrating the immunosuppressive effect of rapamycin when administered during the T cell expansion phase.

To determine the effect of rapamycin treatment during the T cell maintenance phase, mice were adoptively transferred with carboxyfluorescein succinimidyl ester (CFSE)-labeled GP33 epitope-specific memory CD8⁺ T cells (TCR-transgenic P14 cells; Pircher et al., Nature 342:559-561, 1989). CFSE-labeled cells were transferred intravenously via tail vein injection. Mice were either untreated or treated with rapamycin daily for 43 days at a dose of 0.6 mg/kg, beginning one day prior to adoptive transfer (Day −1) (FIG. 3A). On Day 42, the number of transferred virus-specific CD8⁺ T cells in the spleen of treated and untreated mice was determined. To isolate spleen lymphocytes, spleens were homogenized and red blood cells were lysed with 0.83% ammonium chloride. Isolated splenocytes were then evaluated by FACS. As shown in FIG. 3B, rapamycin treatment decreased the number of virus-specific CD8⁺ T cells in the spleen. Proliferation of virus-specific CD8⁺ T cells was also evaluated on Day 42 by detecting fluorescence intensity of CFSE-labeled T cells by FACS. As shown in FIG. 3C, rapamycin treatment reduced the percentage of virus-specific CD8⁺ T cells that divided more than twice (17.8%), relative to untreated mice (42.5%).

To determine the effect of rapamycin treatment during the T cell contraction phase, mice were injected intraperitoneally with 2×10⁵ PFU of LCMV on Day 0 and administered 0.6 mg/kg of rapamycin daily beginning on Day 8 (FIG. 4A). On Day 35 post-infection, the number of virus-specific CD8⁺ T cells in the spleen of rapamycin-treated and untreated mice was determined by FACS using anti-CD8 antibody, anti-CD44 antibody and tetramer staining. Tetramer staining was used to detect GP33, GP276 and NP396 epitope-specific CD8⁺ T cells. To detect NP205 and GP118 epitope-specific CD8⁺ T cells, interferon (IFN)-γ positive cells were measured by intracellular staining after peptide stimulation. As shown in FIG. 4B, rapamycin treatment during the T cell contraction phase did not reduce the number of virus-specific CD8⁺ T cells.

Thus, in accordance with the known immunosuppressive properties of rapamycin, treatment with rapamycin exhibited an immunosuppressive effect during the T cell expansion (FIG. 2) and maintenance (FIG. 3) phases. However, rapamycin treatment did not alter the number of virus-specific CD8⁺ T cells during the contraction phase (FIG. 4).

To examine whether rapamycin treatment effects the quality of virus-specific CD8⁺ T cells during the contraction phase, phenotypic analysis of virus-specific CD8⁺ T cells in spleen, PBMCs and liver was performed by evaluating markers for high quality memory T cells (including CD127^(High), CD62L^(High), KLRG-1^(Low), CD27^(High) and Bcl-2^(High)) by FACS. As shown in FIG. 5, a number of significant differences were identified between control and rapamycin-treated animals. In rapamycin-treated animals, GP33, GP276 and NP396 epitope-specific CD8⁺ T cells phenotypically showed high quality memory T cells (CD127^(High), CD62L^(High), KLRG-1^(Low), CD27^(High), Bcl-2^(High)) compared to untreated animals. In addition to spleen, a similar phenotypic trend of virus-specific CD8⁺ T cells was identified in PBMCs and liver (FIG. 6). In lymph node, no significant change in cell surface markers was observed between untreated and rapamycin-treated animals (FIG. 6). These results were expected because virus-specific CD8⁺ T cells in lymph node typically exhibit a high quality phenotype compared to other tissues. However, in rapamycin-treated animals, Bcl-2 expression was higher than control even in lymph node. Taken together, rapamycin treatment during contraction phase enhanced generation of high quality memory T cells.

The results described above indicate that rapamycin treatment induces high quality memory T cells during the T cell contraction phase. To investigate how rapamycin accumulates high quality memory T cells, CD62L-negative virus-specific effector T cells were transferred into naïve mice as described below and illustrated in FIG. 7A. LCMV-specific transgenic (P14) effector CD8⁺ T cells (Thy-1.1⁺) were isolated from transgenic P14 mice (fully backcrossed with C57BL/6 mice) on Day 8 after LCMV infection. CD62L^(high) cells were depleted from the isolated effector P14 cells using microbeads (Miltenyi Biotec, Auburn, Calif.) (Wherry et al., Nat. Immunol. 4(3):225-234, 2003). The remaining CD62L^(low) effector CD8⁺ T cells were transferred into Thy-1.2⁺ naïve mice. Mice were then left untreated or treated with 0.6 mg/kg rapamycin daily for 26 days. In some experiments, Day 8 effector P14 cells were labeled with CFSE. Virus-specific CD8⁺ T cells in rapamycin-treated mice quickly re-expressed CD62L compared with control mice (FIG. 7B), and the absolute number of CD62L^(High) virus-specific CD8⁺ T cells was greater in rapamycin-treated mice (FIG. 7C). In addition, CD62L re-expression occurred with no or minimal cell division. Therefore, when CFSE-labeled CD62L negative effector T cells were transferred, most cells still retained CFSE 26 days post transfer (FIG. 7D). These results demonstrate that rapamycin treatment enhances CD62L re-expression without cell division during the contraction phase. Furthermore, these data suggest that rapamycin treatment improves differentiation of memory T cells during the contraction phase.

Next, studies were undertaken to determine whether rapamycin-induced memory T cells are effective for rapidly controlling virus infection. To address this issue, the following experiments were designed. CD62L-negative LCMV-specific effector CD8⁺ T cells (Day 8 effector P14 cells) were transferred into naïve mice. These mice were either left untreated or treated with rapamycin for 25 days, then challenged with vaccinia virus (VV) that expresses the GP33 epitope (VVgp33; Wherry et al., Nat. Immunol. 4(3):225-234, 2003) on Day 28 (FIG. 8A). VVgp33 was administered intraperitoneally at a dose of 5×10⁶ PFU. To evaluate the T cell recall response, the percentage of virus-specific CD8⁺ T cells in the spleen was determined by FACS on Day 5 after VV challenge. As shown in FIG. 8B, a greater percentage of virus-specific CD8⁺ T cells (DbGP33 tetramer-positive P14 cells) was detected in rapamycin treated mice (4.93%) relative to untreated mice (1.69%). In addition, the absolute number of DbGP33 tetramer-positive P14 cells was greater in rapamycin-treated mice than in untreated mice (FIG. 8C), suggesting that rapamycin-induced memory T cells expanded rapidly compared with control.

To evaluate the effect of rapamycin treatment on virus infection, viral titers were determined in the ovaries of naïve mice, untreated mice and rapamycin-treated mice on Day 5 post-challenge. As shown in FIG. 8D, rapamycin treatment led to a reduction in viral titer relative to untreated and naïve mice. These results suggest that rapamycin-induced memory CD8⁺ T cells are high quality memory T cells capable of effectively inhibiting virus infection.

In addition to better viral control, homeostatic proliferation is another characteristic of high quality memory T cells. To investigate the ability of rapamycin induced memory T cells to undergo homeostatic proliferation, CFSE-labeled memory T cells derived from rapamycin-treated or untreated mice were adoptively transferred into naïve mice (FIG. 9A). As shown in FIG. 9B, the percentage of divided memory T cells in PBMC was increased with rapamycin treatment. Cell division of P14 memory cells was also evaluated in the spleen 30 days post-transfer. As shown in FIG. 9C, rapamycin treatment increased the percentage of cells that divided more than twice (46.1%), relative to the control (36.8%). These data demonstrate that rapamycin-treated memory T cells exhibit better homeostatic proliferation in both PBMC and spleen, suggesting that rapamycin induces effective memory T cells. Taken together, rapamycin-induced memory CD8⁺ T cells are bona fide high quality memory T cells.

Next, experiments were performed to determine whether rapamycin has any effect on virus-specific CD8⁺ T cells after a recall response. To investigate this, mice were treated with 0.6 mg/kg rapamycin during the contraction phase of a recall response. LCMV-specific memory P14 cells were transferred into naïve mice on Day −1. On Day 0, mice were infected with 5×10⁶ PFU VVgp33. Mice were either untreated or treated with rapamycin each day starting on Day 8 after VV infection (FIG. 10A). The number of P14 cells in the spleen of untreated and rapamycin-treated mice was determined on Day 31 post-infection by FACS. As shown in FIG. 10B and FIG. 10C, the number of virus-specific CD8⁺ T cells was similar between control and rapamycin-treated animals and there was no significant difference in CD127 and CD62L expression. However, expression of KLRG-1 was lower and expression of CD27 and Bcl-2 was higher on virus-specific CD8⁺ T cells from rapamycin-treated mice, relative to control mice (FIG. 10C). These results suggest that rapamycin enhances high quality memory T cells during the contraction phase of T cell recall responses.

Example 2 Low Dose Rapamycin Treatment Enhances the Number of Antigen-Specific CD8⁺ T Cells and Induces High Quality Memory T Cells

As described above, rapamycin treatment during the T cell expansion phase inhibits antigen-driven T cell proliferation. This example describes the effect of a lower dose of rapamycin on T cell responses. In particular, this example demonstrates that low dose rapamycin treatment (i) enhances the number of virus-specific CD8⁺ T cells; (ii) induces high quality memory T cells during a primary T cell response; (iii) induces high quality memory T cells during a recall response; and (iv) induces high quality memory T cells upon immunization with a non-infectious immunogen.

Mice were injected intraperitoneally with 2×10⁶ PFU LCMV on Day 0 and treated daily with a low dose of rapamycin (0.075 mg/kg, which results in a blood concentration of approximately 5-20 ng/ml) beginning one day prior to infection (Day −1) (FIG. 11A). To evaluate the number of virus-specific CD8⁺ T cells in untreated and rapamycin-treated mice, PBMCs were isolated and subjected to FACS analysis. As shown in FIG. 11B, a similar number of GP33 epitope-specific CD8⁺ T cells was detected in PBMCs from treated and untreated mice isolated on Day 8 post-infection. However, mice treated with low dose rapamycin maintained a higher number of GP33 epitope-specific CD8⁺ T cells compared to untreated animals from Day 8 until the conclusion of the 30-day evaluation period. Also examined was the number of virus-specific CD8⁺ T cells in the spleen of untreated and rapamycin-treated mice 35 days post-infection. Tetramer staining was used to detect GP33, GP276 and NP396 epitope-specific CD8⁺ T cells. For NP205 and GP118 epitope-specific CD8⁺ T cells, IFN-γ positive cells were measured by intracellular staining after peptide stimulation. As shown in FIG. 11C, rapamycin treatment enhanced the number of all epitope-specific CD8⁺ T cells examined.

To investigate the quality of virus-specific CD8⁺ T cells in low dose rapamycin-treated mice, phenotypic analysis of T cells was performed by FACS as described above. As shown in FIG. 12, there were significant differences between control and rapamycin-treated animals. In treated animals, virus-specific CD8⁺ T cells exhibited a CD127^(High) CD62L^(High) KLRG-1^(Low) Bcl-2^(High) phenotype compared to untreated mice (FIG. 12A and FIG. 12B). These differences were detected by Day 8 post-infection (FIG. 12C). These data suggest that rapamycin regulates phenotypic changes during T cell differentiation. In addition, these results suggest that low dose rapamycin treatment induces high quality memory T cells.

Next, the effect of low dose rapamycin treatment on virus-specific CD8⁺ T cells after a recall response was evaluated. To investigate this, mice were treated with a low dose of rapamycin (0.075 mg/kg) during recall responses. Thy-1.1⁺ P14 memory cells were adoptively transferred into Thy-1.2⁺ recipient mice and rapamycin treatment was initiated on the same day (Day −1). The next day (Day 0), recipient mice were injected intraperitoneally with 2×10⁶ PFU LCMV (FIG. 13A). The percentage of LCMV-specific CD8⁺ T cells in PBMCs isolated from treated and untreated mice on Days 8, 14, 22 and 35 was evaluated by FACS. As shown in FIG. 13B, the percentage of virus-specific CD8⁺ T cells was greater in rapamycin treated animals than in control mice at each day tested. Moreover, rapamycin treatment enhanced expression of CD127 and CD62L (FIG. 13C). These results indicate that low dose rapamycin induces high quality memory T cells during recall responses as well as primary responses.

To determine whether low dose rapamycin treatment has an effect on T cell responses against noninfectious immunogens, virus-like particles (VLPs) that present GP33 epitope were used to immunize mice (Storni et al., J. Immunol. 168(6):2880-2886, 2002; Storni et al., J. Immunol. 171(2):795-801, 2003). Mice were immunized with 50 μg of VLPs by subcutaneous injection, and mice were either untreated or treated with rapamycin beginning one day prior to immunization (Day −1) (FIG. 14A). After VLP immunization, GP33 epitope-specific CD8⁺ T cells expanded similarly in the rapamycin-treated and control groups (FIG. 14B). However, rapamycin-treated mice maintained a higher number of antigen-specific CD8⁺ T cells compared to control in PBMC (FIG. 14B) and spleen (FIG. 14C). In addition, the phenotype of antigen-specific CD8⁺ T cells isolated from the spleen of rapamycin-treated mice 34 days post-infection exhibited markers of high quality memory T cells (CD127^(High), CD62L^(High) KLRG-1^(Low), Bcl-2^(High)) (FIG. 14D and FIG. 14E). These results suggest that low dose rapamycin induces high quality memory T cells not only upon infection, but also upon immunization with non-infectious immunogen.

Example 3 Rapamycin Intrinsically Affects Virus-Specific CD8⁺ T Cells for Generation of High Quality Memory T Cells and Enhances the Number of Virus-Specific Memory CD4⁺ T Cells

It is known in the art that rapamycin inhibits mTOR, which is ubiquitously expressed and plays a role in a number of cellular processes, including translation, cell survival, autophagy and actin cytoskeleton dynamics. Therefore, it is possible that rapamycin not only affects T cells, but also non-T cells in vivo. How rapamycin induces high quality memory T cells in vivo was previously unknown. To test whether generation of high quality memory T cells by rapamycin is a CD8-intrinsic effect, knockdown of rapamycin-related molecules was performed using a retrovirus-based RNA interference (RNAi) system. mTOR is part of two distinct complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2) (FIG. 15). Recent studies suggest that mTORC1 is sensitive to rapamycin. Therefore, to inhibit the mTORC1 pathway, experiments were performed to inhibit expression of raptor, which is part of mTORC1 (FIG. 16A).

Retrovirus encoding a control or raptor shRNA (GCCCGAGTCTGTGAATGTAAT; SEQ ID NO: 1) was constructed by cloning the shRNA into the pMKO.1-GFP retrovirus vector (Addgene, Cambridge, Mass.). Retrovirus was generated by co-transfection of pMKO.1-GFP-raptor (or pMKO.1-GFP-control) and pCL-Eco (packaging vector) plasmid into HEK-293T cells. For transduction, P14 transgenic mice were infected with 1×10⁶ PFU LCMV intravenously. One day later, activated splenocytes were spin-transduced with freshly made retroviral supernatants from HEK-293T cells (90 minutes at 37° C., 3000 rpm). After transduction, transduced splenocytes were adoptively transferred intravenously to naïve recipient mice that were subsequently infected intraperitoneally with LCMV at a dose of 2×10⁵ PFU. Virus-specific memory T cell phenotype in mouse spleen was evaluated in control and raptor RNAi-treated animals 35 days post-infection by FACS. Raptor knockdown resulted in a high quality memory T cell phenotype (CD127^(High), CD62L^(high) KLRG-1^(Low)) in LCMV-infected mice (FIG. 16B).

A FKBP12 knockdown-retrovirus vector was also constructed by cloning the FKBP12 shRNA (GCCAAACTGATAATCTCCTCA; SEQ ID NO: 2) into the pMKO.1-GFP retrovirus vector (Addgene). FKBP12 forms a complex with rapamycin, and this complex inhibits mTORC1 (FIG. 15). Thus, virus-specific CD8⁺ T cells with FKBP12 knockdown should be rapamycin insensitive. To test this hypothesis, retrovirus-transduced LCMV-specific P14 cells were adoptively transferred into naïve mice and mice were then infected with LCMV at a dose of 2×10⁵ PFU. Rapamycin treatment (0.075 mg/kg) was initiated one day prior to infection (FIG. 17A). The phenotypic changes of adoptively transferred P14 cells were evaluated by FACS on Day 16 post-infection in PBMC. As shown in FIG. 17B, the effect of rapamycin treatment was diminished by FKBP12 knockdown. Taken together, these results demonstrate that rapamycin intrinsically affects virus-specific CD8⁺ T cells for generation of high quality memory T cells.

In addition to CD8⁺ T cells, low dose rapamycin treatment enhanced the number of virus-specific memory CD4⁺ T cells (FIG. 18). Mice were infected with 2×10⁵ PFU LCMV on Day 0 and were either untreated or treated with rapamycin beginning one day prior to infection (Day −1). Spleen cells were isolated on Day 35 and stimulated with LCMV GP61 peptide specific for CD4⁺ T cells. Intracellular cytokine (IL-2 and IFN-γ) staining was performed and the cells were subjected to FACS. As shown in FIG. 18, rapamycin treatment resulted in a higher number of IFN-γ⁺ cells upon peptide stimulation relative to cells from untreated mice.

Example 4 Low Dose Rapamycin Treatment Improves Quantity and Quality of Memory T Cells

This example describes the finding that low dose rapamycin treatment improves the quantity and quality of memory T cells generated by recombinant adenovirus serotype 5 (rAd5) that expresses LCMV glycoprotein (rAd5-LCMV-GP). The nucleotide and amino acid sequences of LCMV GP, deposited under GENBANK™ Accession No. M20869 on Aug. 2, 1993, are set forth herein as SEQ ID NOs: 7 and 8, respectively.

Mice were vaccinated with rAd5-LCMV-GP (1×10¹⁰ viral particles) by intramuscular injection on Day 0 and either left untreated or treated with rapamycin at a dose of 0.075 mg/kg from Day −1 to Day 34 (FIG. 19A). The number of DbGP33 tetramer-positive CD8⁺ T cells in the spleen of treated and untreated mice was determined by FACS on Day 35 post-vaccination. As shown in FIG. 19B, rapamycin treatment significantly increased the number of virus-specific CD8⁺ T cells. The phenotype of virus-specific CD8⁺ T cells was also evaluated by FACS (FIG. 19C). In accordance with data described above, CD8⁺ T cells from rapamycin-treated mice exhibited markers of high quality memory T cells (CD127^(High), CD62L^(High), KLRG-1^(Low), Bcl-2^(High)).

Example 5 mTOR Regulates Memory CD8⁺ T Cell Differentiation

Rapamycin is a commonly used immunosuppressive drug in transplant recipients and specifically inhibits the intracellular kinase mTOR (Wullschleger et al., Cell 124:471-484, 2006). Several recent studies have shown that rapamycin has various effects on the immune system such as inhibiting type I interferon production by plasmacytoid dendritic cells (Cao et al., Nat Immunol 9(10):1157-1164, 2008), modulating T cell trafficking (Sinclair et al., Nat Immunol 9(5):513-521, 2008), and regulating Foxp3 expression in regulatory T cells (Sauer et al., Proc Natl Acad Sci USA 105:7797-7802, 2008; Haxhinasto et al., J Exp Med 205:565-574, 2008). However, the role of the mTOR pathway in regulating CD8⁺ T cell responses is not known. To address this issue, the following experiments were performed.

Materials and Methods

Mice, viral infection, VLP, and virus titrations. Twelve- to sixteen-week old C57BL/6j mice were purchased from The Jackson Laboratory (Bar Harbor, Me.). Thy-1.1 P14 transgenic mice bearing the DbGP33-specific TCR were fully backcrossed to C57BL/6 mice in the animal colony. LCMV Armstrong (2×10⁵ PFU, IP) and recombinant vaccinia virus GP33 (VVGP33, 5×10⁶ PFU, IP), which expresses the LCMV GP33 epitope, were used for infection. VVGP33 titers were determined in the ovary by plaque assay as described previously (Wherry et al., Nat Immunol 4, 225-234, 2003). For VLP immunization, mice were subcutaneously administered 50 μg of VLP, which was derived from the hepatitis B core antigen (HBcAg) genetically fused to the LCMV gp33-41 epitope (KAVYNFA™; SEQ ID NO: 9) and packaged with CpG-ODN.

Administration of rapamycin in mice. Rapamycin (Wyeth, Madison, N.J.) was administered to mice IP daily during the treatment period. Three different treatment periods were used: 1) throughout LCMV infection (Day −1 to the memory phase, Day 35 post-infection); 2) the T cell expansion phase (Day −1 to Day 8 post-infection); or 3) T cell contraction phase (Day 8 to the memory phase, Day 35 post-infection). The daily dose of rapamycin was 75 μg/kg (blood levels approximately 5-20 ng/ml) for treatments 1) and 2) and 600 μg/kg (blood levels approximately 40-100 ng/ml) for treatment 3) (the contraction phase treatment) because the higher dose inhibits T cell responses during the expansion phase of the CD8⁺ T cell response (as evidenced by a decrease in antigen-specific CD8⁺ T cells). Control mice received sham treatment during the same time periods described above (daily injection of the buffer without rapamycin).

Rhesus macaques and vaccination. Six colony-bred, SPF Rhesus macaques (Macaca mulatta) were inoculated with DRYVAX™ (Wyeth, Madison, N.J.) by scarification. Briefly, a bifurcated needle was immersed in the vaccine suspension and used to poke the skin 15 consecutive times. At 105 days post DRYVAX™ vaccination, animals were vaccinated with 10⁸ PFU Modified Vaccinia Ankara (MVA) vaccine intramuscularly.

Administration of rapamycin in rhesus macaques. Daily administration of rapamycin (approximately 10-50 μg/kg/day) was given intramuscularly to three of the six DRYVAX™ immunized rhesus macaques approximately 5 days before MVA vaccination. Blood levels of rapamycin were maintained within a range of about 5-15 ng/ml. The other three macaques were left untreated as controls.

Generation and isolation of effector and memory T cell subsets. To generate LCMV-specific P14 effector T cells, mice adoptively transferred with 1×10⁵ P14 naïve T cells were infected with LCMV. On Day 8 post-infection, effector P14 cells were isolated from the spleen, and CD62L-negative CD8⁺ T cells were purified using anti-CD62L magnetic beads and a CD8⁺ T cell isolation kit (Miltenyi Biotec, Auburn, Calif.). These cells were then used for a CD62L conversion experiment and a protective immune response experiment. For the CD62L conversion experiment, CFSE-labeled CD62L-negative P14 effector cells (about 7-10×10⁶ cells) were adoptively transferred into naïve mice. For the protective immune response experiment, 3×10⁵ CD62L-negative P14 effector cells were adoptively transferred into naïve mice, and rapamycin was administered for 25 days. On Day 28 post-transfer, mice were challenged with VVGP33 to examine protective immune responses.

To obtain memory P14 cells generated in rapamycin treated mice, B6 mice adoptively transferred with 1×10⁵ P14 naïve T cells were infected with LCMV, and these mice were then treated with rapamycin from Day −1 to Day 33 post-infection. On Day 34 post-infection, memory P14 T cells generated in the presence of rapamycin were isolated from the spleen. Control memory P14 cells were obtained using the same method without the rapamycin treatment. For the homeostatic experiment, CFSE-labeled memory P14 cells (1×10⁶ cells) obtained from either rapamycin-treated or untreated mice were adoptively transferred into separate naïve recipients. For the recall response experiment, 1×10⁴ P14 memory T cells derived from either rapamycin-treated or untreated mice were adoptively transferred into separate naïve mice, and the day after transfer these mice were infected with VVGP33. To investigate effects of rapamycin during secondary T cell responses, 2.5×10⁴ P14 memory T cells (>60 days post infection) were adoptively transferred into naïve mice, and rapamycin treatment was started. The day after transfer, these mice were infected LCMV.

Flow cytometry. MHC class I tetramers were made as described previously (Murali-Krishna et al., Immunity 8, 177-187, 1998). All antibodies for flow cytometry were purchased from BD Biosciences except for CD127, KLRG-1, and CD27. Antibodies to CD127 and CD27 were purchased from eBiosciences (San Diego, Calif.) and anti-KLRG-1 was purchased from Southern Biotech (Birmingham, Ala.). Single cell suspensions of spleen cells, lymph nodes, livers, or PBMCs from mice were prepared and direct ex-vivo staining was carried out as described previously (Wherry et al., Nat Immunol 4, 225-234, 2003). For in vivo BrdU incorporation, LCMV-infected mice were fed 0.8 mg/ml BrdU in their drinking water every day. BrdU in virus-specific CD8⁺ T cells was measured using the BrdU flow kit (BD Biosciences), according to the manufacturer's instructions. To detect vaccinia virus-specific CD8⁺ T cells generated in rhesus macaques, 1.5×10⁶ PBMCs isolated by density gradient centrifugation were incubated at 37° C. for 15 hours with vaccinia virus at a multiplicity of infection of 1 in a volume of 300 μl RPMI containing 10% heat inactivated FBS. Brefeldin A (5 μg/mL) was added for the final 5 hours of incubation. IFN-γ producing vaccinia virus-specific CD8⁺ T cells were detected by intracellular cytokine staining.

Retrovirus based RNAi. The pMKO.1 GFP retroviral vector (Addgene plasmid 10676, Cambridge, Mass.) was used for these experiments. Double stranded oligonucleotides for short hairpin RNA (shRNA) against mTOR, raptor, and FKBP12 were cloned into pMKO.1 GFP between the AgeI and EcoRI restriction sites. The sequences for mTOR, raptor, FKBP12, S6K1 and eIF4E shRNAs are shown in Table 4.

TABLE 4  shRNAs specific for mTOR, raptor, FKBP12, S6K1 and eIF4E Sense/ SEQ ID Target Antisense Sequence NO: mTOR Sense CCGGGCCAGAATCCATCCATTCATT 10 CTCGAGAATGAATGGATGGATTCTG GCTTTTTG mTOR Antisense AATTCAAAAAGCCAGAATCCATCCA 11 TTCATTCTCGAGAATGAATGGATGG ATTCTGGC Raptor Sense CCGGGCCCGAGTCTGTGAATGTAAT 12 CTCGAGATTACATTCACAGACTCGG GCTTTTTG Raptor Antisense AATTCAAAAAGCCCGAGTCTGTGAA 13 TGTAATCTCGAGATTACATTCACAG ACTCGGGC FKBP12 Sense CCGGGCCAAACTGATAATCTCCTCA 14 CTCGAGTGAGGAGATTATCAGTTTG GCTTTTTG FKBP12 Antisense AATTCAAAAAGCCAAACTGATAATC 15 TCCTCACTCGAGTGAGGAGATTATC AGTTTGGC S6K1 Sense CCGGGCATGGAACATTGTGAGAAAT 16 CTCGAGATTTCTCACAATGTTCCATG CTTTTTG S6K1 Antisense AATTCAAAAAGCATGGAACATTGTG 17 AGAAATCTCGAGATTTCTCACAATG TTCCATGC eIF4E Sense CCGGCCGAAGATAGTGATTGGTTAT 18 CTCGAGATAACCAATCACTATCTTC GGTTTTTG eIF4E Antisense AATTCAAAAACCGAAGATAGTGATT 19 GGTTATCTCGAGATAACCAATCACT ATCTTCGG

Recombinant retrovirus was made by co-transfection with pMKO.1 GFP and pCL-Eco (Imgenex, San Diego, Calif.) in 293T cells using TransIT-293 (Mirus, Madison, Wis.). Forty-eight hours after transfection, culture supernatants were collected. To transduce P14 cells with the recombinant retrovirus, P14 transgenic mice were infected with 1×10⁶ PFU of LCMV intravenously. After 24 hours, P14 transgenic spleen cells were isolated and then spin-transduced at 37° C. for 90 minutes with freshly collected retrovirus containing 8 μg/ml of polybrene (Sigma, St. Louis, Mo.). Retroviral transduced P14 spleen cells (5×10⁵) were adoptively transferred into naïve mice, followed by LCMV infection (2×10⁵ PFU, IP). The GFP⁺ P14 CD8⁺ T cells were purified by FACS on Day 7 or 8 post-infection, and protein expression levels were analyzed by western blotting. Expression of mTOR, raptor, FKBP12, S6K1 and eIF4E was significantly reduced in cells transduced with retrovirus containing the respective shRNAs.

Results

The role of the mTOR pathway in regulating CD8⁺ T cell responses is not well understood. To address this issue, B6 mice were treated with rapamycin during the course of an acute LCMV infection and the virus-specific CD8⁺ T cell response was monitored (FIG. 20A). It was observed that rapamycin enhanced the LCMV-specific CD8⁺ T cell response. Increased numbers of antigen-specific CD8⁺ T cells were seen in both lymphoid and non-lymphoid tissues, including in PBMCs (FIG. 20A), spleen, lymph nodes and liver. The striking thing about this result was the decreased contraction of the T cell response in the rapamycin treated group. Similar frequencies of virus-specific effector CD8⁺ T cells were observed in both groups of mice at the peak of the T cell response on Day 8 post-infection, but there was minimal contraction of the T cells in the rapamycin-treated group (FIG. 20A). To determine whether the decreased T cell contraction seen between about Days 8-30 post-infection in the rapamycin-treated group was due to increased cell proliferation and/or reduced cell death, mice were infected with LCMV in the presence or absence of rapamycin and then given BrdU during the T cell contraction phase from approximately Days 10-22. It was found that there was minimal incorporation of BrdU by antigen-specific CD8⁺ T cells in either group of mice, indicating that the decreased contraction of T cells in the presence of rapamycin was not due to increased cell proliferation. Thus, it appears that the major effect of rapamycin is to enhance the survival of antigen-specific CD8⁺ T cells.

Next, the phenotype of the memory CD8⁺ T cells present in the two groups of mice at Day 36 post-infection was examined (FIG. 20B). To investigate this, phenotypic analysis of virus-specific memory CD8⁺ T cells was performed using four markers that are useful in defining memory CD8⁺ T cells: CD127 (IL-7 receptor α and essential for memory T cell maintenance; Kaech et al., Nat Immunol 4:1191-1198, 2003; Huster et al., Proc Natl Acad Sci USA 101:5610-5615, 2004; Schluns et al., Nat Immunol 1:426-432, 2000; Tan et al., J Exp Med 195:1523-32, 2002); CD62L (lymph node homing receptor and associated with high proliferative capacity; Wherry et al., Nat Immunol 4, 225-234, 2003); KLRG-1 (inversely-correlated with long lived memory cells; Sarkar et al., J Exp Med 205(3):625-40, 2008; Joshi et al., Immunity 27: 281-295, 2007); and Bcl-2 (anti-apoptotic and expressed at high levels in memory T cells; Schluns et al., Nat Immunol 1:426-432, 2000). Memory CD8⁺ T cells generated in the presence of rapamycin expressed higher levels of CD127, CD62L, and Bcl-2, and had a higher frequency of KLRG-1^(Low) cells compared to control mice (FIG. 20B). These data strongly suggest that inhibition of the mTOR pathway using rapamycin not only increases the magnitude of the virus-specific CD8⁺ T cell response (FIG. 20A), but also improves the functional qualities of the memory CD8⁺ T cells since memory cells with the CD127^(High) CD62L^(High)Bcl-2^(High) and KLRG-1^(Low) phenotype are associated with long-lived protective immunity (Wherry et al., Nat Immunol 4, 225-234, 2003; Sarkar et al., J Exp Med 205(3):625-40, 2008; Joshi et al., Immunity 27: 281-295, 2007). To directly test this, the ability of these memory CD8⁺ T cells to undergo homeostatic proliferation, a property essential for long-term memory maintenance, and to make recall responses upon re-exposure to antigen, was examined. As shown in FIG. 20C and FIG. 20D, virus-specific memory CD8⁺ T cells generated in mice treated with rapamycin were superior to memory cells generated in untreated mice in both of these hallmark memory properties.

In the experiment shown in FIG. 20, mice were continuously treated with rapamycin during the entire course of the T cell response (Day −1 to 35 post-infection). It was next examined how rapamycin would affect the CD8⁺ T cell response if it was only given during the T cell expansion phase (Days −1 to 8 post-infection). These results (FIGS. 21A and 21B) were strikingly similar to what was observed earlier (FIG. 20A); even if the rapamycin treatment was discontinued during the contraction phase (about Days 8-30) there was only minimal death of the effector CD8⁺ T cells generated in the presence of the drug. Previous studies have shown that the Day 8 effector CD8⁺ T cell population consists of two subsets, the terminal effector T cells (CD127^(Low), KLRG-1^(High)) that mostly die over the ensuing 2-4 weeks, and the memory precursor cells (CD127^(High), KLRG-1^(Low)) that mostly survive and further differentiate to give rise to the pool of long-lived memory cells (Kaech et al., Nat Immunol 4:1191-1198, 2003; Sarkar et al., J Exp Med 205(3):625-40, 2008; Joshi et al., Immunity 27: 281-295, 2007). These results suggested that rapamycin enhances the formation of these memory precursor cells. This was indeed the case and Day 8 virus-specific effector CD8⁺ T cells generated in rapamycin-treated mice contained a higher proportion of CD127^(High) KLRG-1^(Low) cells and these cells also expressed higher levels of Bcl-2 (FIG. 21C). However, it was observed that the phenotype of memory CD8⁺ T cells at Day 36 post-infection was similar in the drug-treated and control mice (FIG. 21D). This was different from the results obtained upon continuous rapamycin treatment (compare FIG. 20B versus FIG. 21D). Taken together, these results clearly show that rapamycin enhances the formation of memory precursors during the naïve to effector T cell differentiation phase, but that rapamycin may also regulate the effector to memory transition phase.

To test this hypothesis, mice were treated with rapamycin only during the T cell contraction phase (approximately Days 8-35) following acute LCMV infection (FIG. 22). It was found that the number of memory cells generated were not affected by the drug (FIG. 22A), but the phenotype of these memory CD8⁺ T cells was strikingly different (FIG. 22B). Thus, rapamycin treatment during the effector to memory transition phase enhanced the memory differentiation program resulting in a significantly higher number of virus-specific CD8⁺ T cells with the phenotype characteristic of highly functional memory cells (p value; <0.0001-0.0022) (FIG. 22B).

It was important to determine if this represented cell proliferation and outgrowth of a subset of effector CD8⁺ T cells already expressing these memory markers or if rapamycin truly increased the expression of these markers in the surviving effector T cells during this effector to memory differentiation phase. To address this issue, highly purified (>99.7%) and CFSE-labeled population of Day 8 CD62L^(Low) antigen-specific effector CD8⁺ T cells were transferred into naïve mice and both cell division and memory differentiation of these transferred effector cells was monitored in the presence or absence of rapamycin (FIG. 22C). It was found that there was no cell division during this effector to memory transition phase (approximately Days 1-25 post-transfer), but that the memory T cells that differentiated in the presence of rapamycin re-expressed CD62L much faster (FIG. 22D and FIG. 22E). More importantly, these memory CD8⁺ T cells were functionally superior and exhibited better recall responses and protective immunity (viral control) following challenge with vaccinia virus expressing the LCMV GP33 epitope (FIGS. 22F-22H). Thus, inhibiting mTOR during the effector to memory transition phase improves the functional qualities of memory T cells.

The results described above demonstrate that rapamycin can enhance both the magnitude and quality of the CD8⁺ T cell response following a primary viral infection. It was next examined whether similar effects would be seen during a secondary response. As shown in FIG. 24, rapamycin also enhanced recall responses when drug treatment was only done during secondary LCMV infection. Thus, rapamycin regulates both primary and secondary T cell responses, which has important implications in designing strategies for improving memory T cell qualities during prime-boost vaccine regimens.

To determine if these findings from the mouse model of LCMV infection could be generalized to other systems, the effect of rapamycin treatment following immunization of mice with a non-replicating vaccine was examined. In these experiments, mice were vaccinated with VLPs (virus-like particles) derived from hepatitis B core antigen genetically fused to the LCMV GP33 epitope (Storni et al., J Immunol 172:1777-1785, 2004). Rapamycin again enhanced both the magnitude and the quality of the VLP-induced memory CD8⁺ T cells. It should be noted that the effects of rapamycin treatment were very long-lasting; memory T cell numbers remained 10-fold higher even 165 days after stopping the drug treatment.

The applicability of this approach was also tested in a non-human primate model. Rhesus macaques previously immunized with vaccinia virus were boosted with MVA in the presence or absence of rapamycin and antigen-specific CD8⁺ T cell responses were analyzed by intracellular IFN-γ staining. Clear differences were found in frequencies of antigen-specific CD8⁺ T cells between rapamycin-treated and untreated monkeys. In the presence of rapamycin, maintenance of a higher number of memory CD8⁺ T cells was observed (FIG. 25A and FIG. 25B) and slower T cell contraction was evident compared to control animals (FIG. 25C). These results demonstrate that rapamycin enhances T cell immunity in both mice and non-human primates following vaccination with either live or inactivated vaccines.

These results clearly establish that mTOR is a major regulator of memory CD8⁺ T cell differentiation. However, one unanswered question is whether mTOR is acting intrinsically in antigen-specific CD8⁺ T cells to regulate memory differentiation or if the observed effects of rapamycin on memory formation are mediated by some other cells of the immune system. It is important to resolve this issue since mTOR is ubiquitously expressed by many cells and several recent studies have shown that rapamycin can modulate the functional properties of several other cells of the immune system (Cao et al., Nat Immunol 9(10):1157-1164, 2008; Sauer et al., Proc Natl Acad Sci USA 105:7797-7802, 2008; Haxhinasto et al., J Exp Med 205:565-574, 2008; Ohtani et al., Blood 112:635-643, 2008; Weichhart et al., Immunity 29(4):565-577, 2008).

To address this question, a retrovirus-based RNA interference (RNAi) system was used to specifically knock-down various genes of the mTOR pathway (mTOR, raptor, S6K1, eIF4E, and FKBP12) in antigen-specific CD8⁺ T cells. Retroviruses marked by GFP and expressing RNAi for a particular gene or a control retrovirus were used to infect LCMV-specific transgenic CD8⁺ T cells (P14 cells) and these transduced cells were then adoptively transferred into naïve mice, followed by LCMV infection. This system allowed for comparison of the phenotypic changes that occur during memory T cell differentiation in GFP-positive retrovirus-transduced versus GFP-negative non-transduced antigen-specific CD8⁺ T cells in the same environment (i.e., the same mouse). Thus, any differences in memory differentiation that are seen between these two cell populations can be ascribed to the intrinsic effects of that particular gene in antigen-specific T cells.

First, mTOR itself was knocked down in antigen-specific CD8⁺ T cells. It was found that mTOR RNAi retrovirus-transduced GFP⁺ P14 cells showed significantly higher expression of the canonical memory T cell markers (CD127, CD62L, Bcl-2, CD27) and lower expression of KLRG-1 compared to non-transduced or control vector-transduced P14 cells (FIG. 23A). These data show that mTOR acts intrinsically in antigen-specific CD8⁺ T cells to regulate memory differentiation. However, since mTOR forms two distinct complexes, the rapamycin-sensitive mTOR complex 1 (mTORC1) and the rapamycin-insensitive mTORC2 (see FIG. 15 and Wullschleger et al., Cell 124:471-484, 2006), mTOR knockdown does not completely mimic rapamycin treatment. To distinguish between these two pathways, the raptor gene, which is an essential component of the mTORC1 complex (Hara et al., Cell 110:177-189, 2002; Kim et al., Cell 110:163-175, 2002) was knocked down. As shown in FIG. 23B, inhibition of raptor in antigen-specific T cells gave results identical to what was observed upon knockdown of mTOR identifying the mTORC1 complex as the regulator of memory differentiation.

To gain more insight into mechanisms by which mTOR regulates memory formation, the roles of S6K1 and eIF4E were examined. It was found that knockdown of these mTORC1 downstream effectors significantly enhanced memory CD8⁺ T cell differentiation. Thus, these results show that mTOR is exerting its effect through these two downstream molecules.

To further explore the role of mTOR in T cell intrinsic versus external effects on memory differentiation, rapamycin-insensitive antigen-specific CD8⁺ T cells were generated by knockdown of the FKBP12 protein. This intracellular protein binds rapamycin and it is this FKBP12—rapamycin complex that inhibits the mTORC1 pathway. Thus, by knocking down FKBP12 in P14 CD8 cells, these cells were made insensitive to any intrinsic effects of rapamycin, but the drug could still act effectively on all the other cells in the mouse. This system allows one to examine if inhibition of mTOR in other cells can effect memory CD8⁺ T cell differentiation. As shown in FIG. 23C, inhibiting mTOR in other cells when the antigen-specific cells themselves were rapamycin-insensitive did not affect memory differentiation. The effect of rapamycin on memory differentiation almost disappeared upon knockdown of FKBP12 from the P14 cells and these cells did not show increased expression of the characteristic memory markers (e.g., CD127, CD62L, Bcl2) (see last column of the figures in FIG. 23C). Thus, taken together the results shown in FIGS. 23A-23C establish that mTOR not only acts intrinsically in antigen-specific CD8⁺ T cells, but that inhibiting mTOR in other cells has minimal to no effect on memory T cell differentiation.

During the past few years considerable progress has been made in understanding the lineage relationships between naïve, effector and memory T cells and in defining the phenotypic and functional changes that underlie memory CD8⁺ T cell differentiation (Williams et al., Annu Rev Immunol 25:171-192, 2007); Kaech et al., Immunity 27, 393-405, 2007). However, much less is known about the intracellular molecules and pathways that regulate the generation of memory T cells. In this example, a molecular pathway has been identified that regulates memory T cell differentiation. In addition, these findings provide a strategy for modulating the formation of memory cells. In particular, the ability to increase the functional qualities of memory T cells provides a new approach for enhancing the efficacy of vaccines against infectious diseases and cancer.

Example 6 Rapamycin Treatment with Hepatitis B Virus (HBV) Vaccination

This example describes the use of rapamycin in conjunction with the HBV vaccine to enhance immunological memory specific for HBV, thereby minimizing the need for booster immunizations. Currently, it is recommended that the HBV vaccine be administered in three doses. For infants, the first dose is typically administered at birth, followed by booster doses at 1-2 months and at 6-18 months. For adults, booster doses of the HBV vaccine are recommended 1-2 months and 4-6 months following primary immunization.

An adult subject with no prior exposure to HBV is administered a primary dose of HBV vaccine RECOMBIVAX HB™. Beginning on the day of immunization, the subject is orally administered rapamycin (in either tablet or liquid form) daily for 7 days. HBV immune responses can be evaluated in the subject following primary immunization and administration of rapamycin to determine whether a booster dose of HBV vaccine is required to establish sufficient immunological memory to prevent HBV infection.

Example 7 Rapamycin Treatment of a Subject with Chronic Hepatitis C Virus Infection

This example describes the use of rapamycin in the treatment of a subject diagnosed with chronic hepatitis C virus (HCV) infection. Patients with chronic HCV infection are at risk of developing liver inflammation, fibrosis, cirrhosis or liver cancer. Thus, it is desirable to treat HCV patients to reduce or eliminate HCV titers, replication and spread.

The subject diagnosed with chronic HCV is treated with a low dose of rapamycin (approximately 0.075 mg/kg) daily for 30 days. Rapamycin is administered orally (in either tablet or liquid form). HCV-specific immune responses, or the titer of HCV in the subject, can be evaluated after 30 days to determine if additional doses of rapamycin are required. The subject is optionally treated with anti-viral medication, such as interferon alpha or ribavirin.

Example 8 Rapamycin Treatment of a Subject Infected with Influenza Virus

This example describes the use of rapamycin in the treatment of a subject with an acute influenza virus infection. To enhance the immune responses against influenza virus, a subject with an acute infection is administered rapamycin within 15 days of exposure to the virus. The subject is administered rapamycin daily at a dose of approximately 0.6 mg/kg. Rapamycin is administered orally (in either tablet or liquid form). Rapamycin is administered daily for approximately 14 days, or until the symptoms of infection have cleared. The subject is optionally treated with anti-flu virus medication, such as oseltamivir, zanamavir, amantadine or rimantadine.

This disclosure provides a method of enhancing antigen-specific T cell immune responses in a subject. It will be apparent that the precise details of the methods described may be varied or modified without departing from the spirit of the described disclosure. We claim all such modifications and variations that fall within the scope and spirit of the claims below. 

1. A method of treating cancer comprising administering an effective amount of a composition comprising an mTOR inhibitor in combination with a purified antigen or a vaccine.
 2. The method of claim 1, wherein the purified antigen is a tumor antigen.
 3. The method of claim 2, wherein the tumor is a hematologic cancer or a solid tumor.
 4. The method of claim 3, wherein the hematologic cancer is a leukemia or a lymphoma.
 5. The method of claim 3, wherein the solid tumor is a carcinoma, melanoma, sarcoma or central nervous system tumor.
 6. The method of claim 1, wherein the tumor antigen is selected from fibroblast growth factor 5, tyrosinase, epithelial tumor antigen (ETA), carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alphafetoprotein (AFP), human telomerase reverse transcriptase, thyroglobulin, intestinal carboxyl esterase, macrophage colony stimulating factor, prostase, prostate-specific antigen (PSA), human epidermal growth factor receptor 2, survivin, telomerase, prostate-carcinoma tumor antigen-I, neutrophil elastase, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, and mesothelin,
 7. The method of claim 1, wherein the mTOR inhibitor is rapamycin or analogs. 